Methods and compositions for producing stem cell derived dopaminergic cells for use in treatment of neurodegenerative diseases

ABSTRACT

The present disclosure relates to methods for producing dopaminergic cells and evaluating their functionality. When pluripotent human embryonic stem cells are cultured on plates coated with laminin-111, laminin-121, laminin-521, laminin-421, or laminin-511 in cell culture medium containing a GSK3 inhibitor and a TGF-β inhibitor as well as timely administered fibroblast growth factor, desired neural cells are produced at far higher rates. Useful cell culture kits for producing such dopaminergic cells are also described herein, as are methods of using such cells for stem cell therapy.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Patent ApplicationSer. No. 62/300,000, filed Feb. 25, 2016; and to U.S. Provisional PatentApplication Ser. No. 62/182,051, filed Jun. 19, 2015; and to U.S.Provisional Patent Application Ser. No. 62/145,467, filed Apr. 9, 2015;the disclosures of which are hereby fully incorporated by reference.

BACKGROUND

This application incorporates by reference the material in the ASCIItext file named “Seq_List_LCTI_200040USP3_ST25.txt”, which was createdon Feb. 10, 2016, and has a file size of 8,781 bytes.

The present disclosure relates to methods for producing certain desireddopaminergic cells from human pluripotent stem cells (hESCs) and forpredicting their phenotypic maturation after transplantation to thebrain based on molecular markers. These dopaminergic cells can then beused in stem cell based therapies such as for treating neurodegenerativediseases including Parkinson's disease. Also disclosed are kits forpracticing the methods. Very generally, the stem cells are cultured on asubstrate of laminin-111 (or other recombinantly produced laminins) andexposed to a variety of cell culture mediums to produce the dopaminergiccells with much higher efficiency than previously attained.

Laminins are a family of heterotrimeric glycoproteins that resideprimarily in the basal lamina. They function via binding interactionswith neighboring cell receptors on the one side and by binding to otherlaminin molecules or other matrix proteins such as collagens, nidogensor proteoglycans. The laminin molecules are also important signalingmolecules that can strongly influence cellular behavior and function.Laminins are important in both maintaining cell/tissue phenotype, aswell as in promoting cell growth and differentiation in tissue repairand development.

Laminins are large, multi-domain proteins, with a common structuralorganization. A laminin protein molecule comprises one α-chain subunit,one β-chain subunit, and one γ-chain subunit, all joined together in atrimer through a coiled-coil domain. The twelve known laminin subunitchains can form at least 15 trimeric laminin types in native tissues.Within the trimeric laminin structures are identifiable domains thatpossess binding activity towards other laminin and basal laminamolecules, and membrane-bound receptors. FIG. 1 shows the three lamininchain subunits separately. For example, domains VI, IVb, and IVa formglobular structures, and domains V, IIIb, and IIIa (which containcysteine-rich EGF-like elements) form rod-like structures. Domains I andII of the three chains participate in the formation of a triple-strandedcoiled-coil structure (the long arm).

There exist five different alpha chains, three beta chains and threegamma chains that in human tissues have been found in at least fifteendifferent combinations. These molecules are termed laminin-1 tolaminin-15 based on their historical discovery, but an alternativenomenclature describes the isoforms based on their chain composition,e.g. laminin-111 (laminin-1) that contains alpha-1, beta-1 and gamma-1chains. Four structurally defined family groups of laminins have beenidentified. The first group of five identified laminin molecules allshare the β1 and γ1 chains, and vary by their α-chain composition (α1 toα5 chain). The second group of five identified laminin molecules,including laminin-521, all share the β2 and γ1 chain, and again vary bytheir α-chain composition. The third group of identified lamininmolecules has one identified member, laminin-332, with a chaincomposition of α3β3γ2. The fourth group of identified laminin moleculeshas one identified member, laminin-213, with the newly identified γ3chain (α2β1γ3).

Human embryonic stem (hES) cells hold promise for the development ofregenerative medicine for a variety of diseases, such as spinal cord andcardiac injuries, type I diabetes and neurodegenerative disorders likeParkinson's Disease. A stem cell is an undifferentiated cell from whichspecialized cells are subsequently derived. Embryonic stem cells possessextensive self-renewal capacity and pluripotency with the potential todifferentiate into cells of all three germ layers. They are useful fortherapeutic purposes and may provide unlimited sources of cells fortissue replacement therapies, drug screening, functional genomics andproteomics.

Stem cell based therapies and treatments for neurodegenerative diseasesare expected to reach clinical trials soon. However, a major hurdleremains in generating standardized good manufacturing practices(GMP)-grade human pluripotent stem (hPS) cell-based progenitors thatupon transplantation will mature and function in the adult brain. Ascells are transplanted as immature progenitors and full maturation intofunctionally integrated neurons requires 6 months or longer in vivo,transplanted cells cannot be assessed for functionality prior totransplantation, and there is a lack of markers that reliably predictyield and maturation of the immature progenitors.

As a surrogate for markers predicting functional properties, the fieldhas relied upon assessing transplanted progenitors by expression ofgenes and proteins developmentally linked to the generation of certainneuronal subtypes. Since it is uncertain if these markers are predictiveof terminal differentiation and functional maturation, the progenitorsmust therefore be taken through lengthy in vivo functional assessment inorder to control for batch-to-batch variation and therapeutic efficacy.This can pose a significant hurdle for the generation of cells forlarger cohorts of patients and for launching a standardized stem cellproduct to the clinic.

To reduce the in vivo studies needed to be performed during the celldevelopmental process, it will thus be necessary to identify a validatedset of markers that can predict the in vivo performance of the stem cellproduct prior to transplantation. Being able to predict an in vivo graftoutcome at the progenitor stage may also lead to the production ofstandardized cell products from variable input sources, such as frompatient-derived cells or hPS cell banks with HLA-haplotyped donors.

Parkinson's disease is a particularly interesting target for stem cellbased therapies due to the relatively focal degeneration of a specifictype of mesencephalic dopamine (mesDA) neuron. Proof-of-concept thatcell replacement therapy for Parkinson's disease can be successful hasbeen obtained in a number of clinical trials using fetal cells.

Recent developments have resulted in a better understanding of thedevelopmental and cellular ontogeny of mesDA neurons from the floorplate of the ventral mesencephalon, and this knowledge has materializedinto research grade differentiation protocols that result in theformation of ventral mesencephalon progenitors from hPS cells. Incontrast to older protocols, these dopaminergic neurons of ventralmesencephalon origin have been shown to survive, mature, and acquireappropriate functional properties in animal models of Parkinson'sdisease. Moreover, grafts generated from these protocols do not resultin cell overgrowths or tumor formation, thus making them suitablecandidate cells for stem cell replacement therapies.

In current ventral mesencephalon differentiation protocols,mesencephalic floor plate markers LMX1A, FOXA2, OTX2, and CORIN arecommonly used to confirm the mesDA identity of progenitors in vitroprior to grafting, but a new study has revealed that these and severalother commonly used ventral mesencephalon markers are also co-expressedin diencephalic progenitors of the subthalamic nucleus. Thus, theyappear to be suboptimal markers in protocols for the generation ofenriched mesDA neurons, as they are clearly not specific to the mesDAdomain.

For the purposes of regenerative medicine and for modeling human neuralcells, there is a desire to develop methods that allow derivation andculturing of pluripotent stem cells under chemically defined, xeno-free,pathogen-free, and for reproducible differentiation of these cells intoneural cells with regenerative capacity. Desirably, such methods shouldprovide large quantities of such differentiated cells. Further, it wouldbe desirable to develop methods for predicting successful graft outcomesof transplanted progenitors in an animal model.

BRIEF DESCRIPTION

The present disclosure provides methods for producing certain stem cellderived desired dopaminergic cells as well as methods for evaluatingtheir functionality after transplantation. These dopaminergic cells canthen be used in stem cell based therapies such as for treatingneurodegenerative diseases including Parkinson's disease. In furtheraspects, the present disclosure provides a kit for producingdopaminergic cells from embryonic stem cells.

The present disclosure also provides methods for culturing certaindesired stem cells in monolayer cultures which facilitates cellularhomogeneity, removal of the stem cells from a cell culture plate orother cellular support in single cell suspension, and replating stemcells in single cell suspension for passaging and expansion insignificant dilutions that enable expansion of stem cell cultures andlarge scale production of such cells.

In some aspects, the disclosure describes the plating of pluripotentstem cells on a substrate of Laminin-111 or Laminin-121, and culturingthe cells using several different cell culture mediums to obtaindopaminergic cells, particularly caudalized dopaminergic progenitorcells. The cells may be passaged with EDTA prior to plating.

In various embodiments, as many as six different cell culture mediumscan be used. In others, only three or four different mediums need to beused.

The stem cells can be cultured in a primary medium comprising N2 medium(N2M), a TGF-β inhibitor, noggin, sonic hedgehog protein, and a GSK3inhibitor. A ROCK inhibitor may be added to the medium for the first24-72 hours

The primary medium may then be removed and a secondary medium is added,the secondary medium comprising N2 medium and a fibroblast growth factor(FGF). The FGF can be FGF8b. The secondary medium may be added about 156hours to about 228 hours after the plating.

The secondary medium can then be removed and the stem cells replated.The replating can occur about 252 hours to about 276 hours after theplating.

The replating can occur using a tertiary medium that comprises a B27medium, a ROCK inhibitor, the FGF, a brain derived neurotrophic factor(BDNF), and ascorbic acid.

The stem cells may then be cultured in a quaternary medium, thequaternary medium comprising a B27 medium, the FGF, a brain derivedneurotrophic factor (BDNF), and ascorbic acid. The stem cells can becultured in the quaternary medium until about 372 hours to about 396hours after the original plating (not the replating). Put another way,the replated stem cells are cultured in the quaternary medium for a timeperiod of about 108 hours to about 132 hours.

In some other embodiments, the first medium includes a neural inductionmedium (NIM) or an N2 medium, a ROCK inhibitor, a TGFβ inhibitor, a GSK3inhibitor, and optionally a sonic hedgehog protein and a noggin protein.

According to some embodiments, the second medium includes (i) NIM or anN2 medium; a TGF-β inhibitor, and a GSK3 inhibitor, and optionally asonic hedgehog protein and a noggin protein. The second medium does notcontain the ROCK inhibitor of the first medium. The second medium may beadded about 36 hours to about 60 hours after plating.

According to some other embodiments, the third medium comprises a neuralproliferation medium (NPM) and a TGF-β inhibitor; and optionally theGSK3 inhibitor and sonic hedgehog protein. The third medium may be addedabout 84 hours to about 108 hours after the first plating, and can berenewed about 156 hours to about 180 hours after the first plating. Thethird medium may be removed after about 156 hours to about 228 hoursafter the first plating.

In further embodiments, the fourth medium comprises (i) a neuralproliferation medium (NPM) or an N2 medium; and (ii) a fibroblast growthfactor (FGF). The fourth medium may be added about 156 hours to about228 hours after the first plating. The fourth medium may be removedafter about 36 hours to about 108 hours exposure, i.e. about 252 hoursto about 276 hours after the original plating. The cells are thenreplated on a second plate coated with laminin-111, laminin-121,laminin-521, laminin-421, or laminin-511.

A fifth medium may be used that comprises a B27 medium; a brain derivedneurotrophic factor (BDNF); ascorbic acid (AA); a glial cellline-derived neurotrophic factor (GDNF); and a fibroblast growth factor(FGF). The fifth medium can be renewed about 324 hours to about 348hours after the original plating. After about 14 days to 16 days, i.e.about 336 hours to about 384 hours, the progenitor cells are obtained.If additional time is desired, a sixth cell culture medium can be usedthat comprises a B27 medium; a brain derived neurotrophic factor (BDNF);ascorbic acid (AA); a glial cell line-derived neurotrophic factor(GDNF), a cAMP agonist (e.g. dibutyryl-cAMP) and a gamma-secretaseinhibitor (DAPT); and does not contain a fibroblast growth factor (FGF).

Also disclosed herein are methods for providing caudalized dopaminergicprogenitor cells with a high probability of successful graft outcome,comprising: plating embryonic stem cells on a first substrate coatedwith laminin-111, laminin-121, laminin-521, laminin-421, or laminin-511to produce dopaminergic progenitor cells; identifying dopaminergicprogenitor cells that express caudal ventral midbrain markers; andisolating the identified dopaminergic progenitor cells from the otherdopaminergic progenitor cells on the substrate to obtain the caudalizeddopaminergic progenitor cells with a high probability of successfulgraft outcome.

The methods may further comprise grafting the caudalized dopaminergicprogenitor cells into a brain of a mammal. The mammal can be a human.This grafting can be performed for the treatment of a neurodegenerativedisease, such as Parkinson's disease.

The step of identifying ventral midbrain progenitors can be defined byco-expression of OTX2, FOXA2 and LMX1A/B. The step of identifyingdopaminergic progenitor cells within the ventral midbrain domain can beperformed by identifying cells that express high levels of EN1, SPRY1,WNT1, CNPY1, PAX8, ETV5, PAX5, FGF8, SPS, or TLE4. More particularly,the step of identifying dopaminergic cells can be performed byidentifying cells that express high levels of EN1, SPRY1, PAX8, CNPY1,and ETV5.

The step of identifying dopaminergic progenitor cells within ventralmidbrain cultures can further include excluding cells that express highlevels of EPHA3, FEZF1, WNT7B, BARHL1, BARHL2, FOXG1, SIX3, HOXA2, GBX2,or PAX6 and by identifying cells that express only low to intermediatelevels of CORIN and FOXP2.

The present disclosure also describes a kit for producing dopaminergiccells in vitro. The kit includes: a cell culture plate with a coating oflaminin-111, laminin-121, laminin-521, laminin-421, or laminin-511; acell culture medium; a GSK3 inhibitor; sonic hedgehog protein; a ROCKinhibitor; a TGF-β inhibitor; a fibroblast growth factor (FGF); a brainderived neurotrophic factor (BDNF); and ascorbic acid (AA).

These and other non-limiting characteristics of the disclosure are moreparticularly disclosed below.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee.

The following is a brief description of the drawings, which arepresented for the purposes of illustrating the exemplary embodimentsdisclosed herein and not for the purposes of limiting the same.

FIG. 1 shows the structural motifs of laminin alpha (α), beta (β), andgamma (γ) chains. The N-terminal, internal, and C-terminal globulardomains are depicted as white ovals. The coiled-coil forming domains (Iand II) are shown as white rectangles. The rod-like structures (domainsV, IIIb, and IIIa) are depicted as grey rectangles.

FIG. 2 is a graphic representation of some methods of the presentdisclosure, identifying specific ingredients and when they are appliedto the stem cells to achieve the desired effect. This is a GMP-suitabledifferentiation protocol.

FIG. 3 is another graphic presentation of other methods of the presentdisclosure, in which alternative cell culture media (NIM and NPM) areused. NDM medium in this figure is equivalent to B27M

FIGS. 4A-4G are a set images and graphs illustrating that batches ofventral mesencephalic-patterned hESCs give variable outcomes, which arenot correlated with common mesDA markers. Thirty-three (33) groups ofrats were subjected to one-sided dopaminergic lesions with 6-OHDA weregrafted with 28 different batches of VM-patterned hESCs. All grafts werederived from H9 cells.

FIG. 4A is a set of images taken from selected animals after in vivomaturation. The brains were stained for TH (tyrosine hydroxylase)content, revealing varied outcomes of the grafts. FIG. 4B is aquantification of dopaminergic (DA) cell yield in individual animalsacross 33 batches. The y-axis is the number of TH+ cells per 100,000cells transplanted, and runs from 0 to 20,000 in intervals of 4,000,then from 30,000 to 50,000 in intervals of 20,000 at the top. FIG. 4C isa quantification of graft volume in individual animals across 33 animalgroups based on HuNu+ immunostainings. The y-axis is the graft volume incubic millimeters per 100,000 cells transplanted, and runs from 0 to 7in intervals of 1. FIG. 4D is a quantification of DA cell density (i.e.total TH+ cell number per mm³ graft volume) in grafts from individualanimals across 33 groups. The y-axis runs from 0 to 15,000 in intervalsof 3,000. For FIGS. 4B-4D, cell content was normalized to 100,000grafted cells, and horizontal bars indicate means for each batch. FIG.4E is a schematic summary of the study of Example 6.

FIG. 4F is a graphic representation of gene expression of FOXA2, LMX1Aand CORIN in the transplanted cell population on day 16 (day oftransplantation) plotted versus the mean TH+ cell content (i.e. DAyield) in each graft experiment. For the LMX1A graph, the y-axis runsfrom 0 to 6,000 in intervals of 2,000, and the x-axis runs from 0 to10,000 in intervals of 2,500. Spearman correlation: R=0.15, p=0.50. Forthe FOXA2 graph, the y-axis runs from 0 to 1,500 in intervals of 500,and the x-axis runs from 0 to 10,000 in intervals of 2,500. Spearmancorrelation: R=−0.38, p=0.08. For the CORIN graph, the y-axis runs from0 to 15,000 in intervals of 5,000, and the x-axis runs from 0 to 10,000in intervals of 2,500. Spearman correlation: R=−0.17, p=0.37.

FIG. 4G is a graphic representation of the gene expression of TH, NURR1and AADC in the transplanted cell population on day 16 (day oftransplantation) plotted versus the mean TH+ cell content (i.e. DAyield) in each graft experiment. Results from Spearman correlationanalysis (ventral mesencephalic cells only) are given as R and p-valuesin each graph and tendencies of correlation are shown by linearregression lines. For the TH graph, the y-axis runs from 0 to 8,000 inintervals of 2,000, and the x-axis runs from 0 to 8,000 in intervals of2,000. Spearman correlation: R=−0.18, p=0.53. For the NURR1 graph, they-axis runs from 0 to 4,000 in intervals of 1,000, and the x-axis runsfrom 0 to 8,000 in intervals of 2,000. Spearman correlation: R=0.11,p=0.70. For the AADC graph, the y-axis runs from 0 to 600 in intervalsof 200, and the x-axis runs from 0 to 8,000 in intervals of 2,000.Spearman correlation: R=0.31, p=0.28.

FIGS. 5A-5I are a set of images and graphs indicating that RNAsequencing analysis of transplanted cells reveals positive correlationbetween graft TH+ content and markers of the midbrain-hindbrain border(MHB). All grafts were derived from H9 cells. FIG. 5A is a graphicalrepresentation of DA yield divided into DA-high and DA-low groups at 6weeks and >16 weeks. Only experiments with relevant day 16 RNA sampleswere categorized as either high or low. Dopaminergic function of thegrafts was assessed in grafts with long-term maturation (>16 weeks)through amphetamine induced rotation (“−” indicates lack of functionalrecovery, “+” indicates functional recovery, ND indicates notdetermined). The y-axis is the number of TH+ cells per 100,000 cellsgrafted, and runs from 0 to 10,000 in intervals of 5,000. FIG. 5B is aPCA plot of results from RNA sequencing analysis of day 16 cell samplesfrom a revealed clustering of DA-low and DA-high samples on the PC4axis. FIG. 5C is a list of results from Deseq2 analysis of RNAsequencing data from the DA-high versus DA-low cell samples (see boxeddata points in FIG. 5I below). The list shows the 12 genes with highestlog 2 fold change (log 2 FC) and with a p-value of <0.001.

FIG. 5D is a graph of EN1 mRNA levels and FIG. 5E is a graph of PAX8mRNA levels, both measured by qRT-PCR in day 16 transplanted cellbatches. For the EN1 graph, the y-axis runs from 0 to 15,000 inintervals of 5,000, and the x-axis runs from 0 to 8,000 in intervals of2,000. For the PAX8 graph, the y-axis runs from 0 to 150 in intervals of50, and the x-axis runs from 0 to 8,000 in intervals of 2,000. For bothFIGS. 5D-5E, Spearman correlation analysis is given as R and p-values ineach graph and correlations are visualized with linear regression lines.

FIG. 5F is a graphical summary of RNA sequencing correlation analysisshowing positive correlations between TH+ content, graft volume and TH+density and RNA levels of MHB genes and common ventral mesencephalicmarkers. Positive correlation is defined by Spearman correlationanalysis with p<0.05. Genes verified by qRT-PCR are shown in bold. FIG.5G is a graphical representation of a Spearman distance analysis of RNAlevels in cell batches, showing co-regulation of MHB genes, whereasFOXP2, FOXA2, LMX1B, CORIN, LMX1A, and OTX2 are uncoupled or negativelycoupled to the MHB genes cluster. FIG. 5H shows five representativeimages of TH+ neurons from different cell batches with high expressionof predictive markers revealing mature morphology of the grafted cells.Scale bar: 50 μm.

FIG. 5I is a graphical analysis of predictive markers following theDeseq2 analysis of RNA sequencing data from DA-high and DA-low cellsamples. Markers were plotted based on log 2 fold change compared tomean of normalized counts. The box in this figure shows the genes listedin FIG. 5C above.

FIGS. 6A-6F are a set of images and graphs indicating that ventralmesencephalic-patterned hESC cultures contain cells of diencephalic STNfates. FIG. 6A is a set of three graphs showing negative correlationbetween RNA levels of the diencephalic markers FEZF1, WNT7B, and EPHA3in transplanted cells (day 16) and TH+ content in grafts. For the FEZF1graph, the y-axis runs from 0 to 8 in intervals of 2, and the x-axisruns from 0 to 10,000 in intervals of 2,500. R=−0.63, p=0.015. For theWNT7B graph, the y-axis runs from 0 to 0.6 in intervals of 0.2, and thex-axis runs from 0 to 10,000 in intervals of 2,500. Spearmancorrelation: R=−0.54, p=0.024. For the EPHA3 graph, the y-axis runs from0 to 20 in intervals of 5, and the x-axis runs from 0 to 10,000 inintervals of 2,500. Spearman correlation: R=−0.63, p=0.015.

FIG. 6B is a set of images of immunostainings of ventralmesencephalic-patterned hESC cultures (day 16) revealing the presence ofSTN domain fates (BARHL1+/FOXA2+ and PITX2+/LMX1A/B+ cells). FIG. 6C isa schematic overview of expression domains in the diencephalic STNregion and in lateral midbrain domains. FIG. 6D is a set of confocalimages of an 18 week old graft showing the presence of BARHL1+/PITX2+and BARHL1+/PITX2− cells. FIG. 6E is a set of example images of BARHL1+cell content in grafts derived from cell batches with low (left) or high(right) BARHL1 RNA levels at the day of transplantation.

FIG. 6F is a set of graphical representations showing positivecorrelations between BARHL1 and BARHL2 RNA levels at the time oftransplantation (qRT-PCR) and the number of BARHL1+ cells in the maturegrafts. For the BARHL1 graph, the y-axis runs from 0 to 1500 inintervals of 500, and the x-axis runs from 0 to 15,000 in intervals of5,000. Spearman correlation: R=0.89, p=0.03. For the BARHL2 graph, they-axis runs from 0 to 5000 in intervals of 1000, and the x-axis runsfrom 0 to 15,000 in intervals of 5,000. Spearman correlation: R=0.89,p=0.03. For FIGS. 6A and 6F, results from Spearman correlation analysisare given as R and p-values in each graph, and correlations arevisualized with linear regression lines.

FIG. 6G is a set of eight images of immunostainings of ventralmesencephalic-patterned hESC cultures (day 42, similar to FIG. 6B),showing the terminal in vitro differentiation of cultures with STNfates.

FIGS. 7A-7I are a set of images and graphs indicating that timeddelivery of FGF8 to hESCs causes cell fates to switch from diencephalicto caudal ventral mesencephalic progenitors. In vitro studies used datafrom both H9 and RC17 lines.

FIG. 7A is a graphical representation of mRNA levels of FOXG1, SIX3,GBX2, and HOXA2 following qRT-PCR analysis (day 10) afterdifferentiating hESCs treated with FGF8b from days 0-9. For the FOXG1graph, the y-axis runs from 0 to 800 in intervals of 200. For the SIX3graph, the y-axis runs from 0 to 1000 in intervals of 200. For the GBX2graph, the y-axis runs from 0 to 150 in intervals of 50. For the HOXA2graph, the y-axis runs from 0 to 300 in intervals of 100. For all fourgraphs, the x-axis indicates the amount of FGF8b, and is either 0, 100,or 300 ng/m L.

FIG. 7B is a set of four immunostaining images (day 16) revealingpatches of PITX2+ and NKX2.1+ cells and patches of LMX1− cells incultures treated with FGF8b from d0-9. FIG. 7C is a set of nineimmunostaining images illustrating that LMX1+/FOXA2+ ventralmesencephalic phenotype is maintained in cultures treated with FGF8bfrom day 7-16 or 9-16. FIG. 7D is a set of six immunostaining imagesillustrating that day 16 cultures treated with FGF8b from day 9-16 havedecreased levels of BARHL1+ and FOXA2 cells. FIG. 7E is a set of siximmunostaining images illustrating that day 16 cultures treated withFGF8b from day 9-16 have decreased levels of PITX2 but increased levelsof EN1 cells. FIG. 7F is a graphical quantification of FIGS. 7D-7E. They-axis runs from 0 to 100% in intervals of 20. FIG. 7G is a graphicalrepresentation of mRNA levels at day 16 of FOXA2, LMX1A, OTX2, and EN1following PCR analysis. The labels on the y-axis are, from bottom totop, 1, 4, 16, 64, 256, and 1024.

FIG. 7H is a FACS plots of control and FGF8b-treated ventralmesencephalic-patterned cultures (day 16) showing unchanged percentagesof FOXA2+ progenitors. For VM, the values are 94.6±2.7% (mean±SEM). ForVM+FGF8, the values are 95.4±1.3%. For control, the values are 0.3±0.2%,n=3. FIG. 7I is a FACS plot of control and FGF8b-treated ventralmesencephalic-patterned cultures (day 16) showing decreased percentagesof CORIN+ progenitors. For VM, the values are 52.9±4.5%. For VM+FGF8,the values are 28.1±1.8%. For control, the value is 0.0%, n=3.

FIGS. 8A-8K are a set of images and graphs indicating thatdifferentiation of hESCs on a GMP-compatible laminin-matrix produceshigh yield and purity of ventral mesencephalic progenitors. RC17 cellswere used. FIG. 8A is a set of seven images illustrating neuraldifferentiation of hESCs on different laminin subtypes. FIG. 8B is apair of images exhibiting how the culturing of hESCs on LN-111 inpluripotency medium resulted in detachment and formation of spheres,whereas pluripotent cells efficiently attached to the LN-521 matrix.FIG. 8C is a graph comparing the use of LN-111 coated substrates toLN-121 coated substrates, showing the yield of dopaminergic cells isabout equal on either substrate. FIG. 8D is a set of four imagesillustrating that seeding of low density hESCs on LN-111 matrix insupplemented N2 medium resulted in confluent neuralized cultures after 7days of differentiation. FIG. 8E is a graph of the downregulation ofOCT4 and NANOG mRNA levels across three days of differentiation onLN-111. The y-axis runs from 0.0 to 1.0 in intervals of 0.2, and thex-axis runs from 0 to 3 in intervals of 1.

FIG. 8F is a graph of cell yield across different combinations of basicmedium (DMEM/F12+Neurobasal with N2 supplement, N2 supplement, B27supplement, and DMEM/F12+). The y-axis is cell count in millions on day11, and runs from 0 to 200 in intervals of 50.

FIG. 8G is a graphical comparison of cell yield from research-gradeEB-based protocol with the cell yield from the GMP-adapted LN-111protocol shown in FIG. 2. The y-axis is cell count in millions, and runsfrom 0 to 500 in intervals of 100. FIGS. 8H-8K exhibit that terminalmaturation (day 45) of ventral mesencephalic progenitors generated bythe GMP protocol of FIG. 2 resulted in electrophysiologically activeneurons. FIG. 8H is a graph showing representative trace of actionpotentials induced with depolarizing current injections. FIG. 8I is agraph illustrating that some ventral mesencephalic cells showedspontaneous post-synaptic currents indicative of synaptic integration inthe dish. FIG. 8J is a graphical example of rebound depolarization afterbrief membrane depolarization characteristic of dopaminergic phenotype.FIG. 8K is an inset showing respective trace from FIG. 8J on an expandedscale.

FIGS. 9A-9E is a set of images and graphs indicating thatdifferentiation of hESCs from GMP-compatible protocol produces ventralmesencephalic cell batches with reproducibly high expression ofpredictive markers from the caudal ventral mesencephalon. FIG. 9A is aset of three immunostained images taken of cultures differentiatedaccording to the GMP protocol, showing a very high overlap ofLMX1A/FOXA2. FIG. 9B is a set of two FACS plots of OTX2/FOXA2double-labelling by flow cytometry with mean (%)±SEM of replicateexperiments (n=3). For both plots, the y-axis (OTX2-APC) is logarithmic,with the bottom value being 10⁰, and proceeding through 10¹, 10², 10³,10⁴, 10⁵, 10⁶, and 10⁷. The x-axis (FOXA2-PE) is also logarithmic, withthe leftmost value being 10°, and proceeding through 10², 10⁴, and 10⁶.

FIG. 9C is a graphical representation of gene expression levels in humanESCs differentiated according to either research-grade embryoid bodyprotocol or GMP-grade LN-111 protocol. Differentiations towards ventralforebrain (vFB) and ventral hindbrain (vHB) were included as controls.Values are color-coded and normalized to sample with highest expressionfor each gene (=1000). FIGS. 9D-9E are 10 representative images ofadditional grafts from batches containing high levels of caudal VMmarkers. The images of FIG. 9D are of grafted H9 cells, and FIG. 9Eshows RC17 cells, both generated via the GMP-grade protocol.

FIG. 10 is a graphical representation of behavioral recovery in ananimal model of Parkinson's Disease. Rats subjected to unilateral 6-OHDAlesions were assessed for amphetamine-induced rotations before and aftertransplantation with RC17 cells differentiated according to the LN-111GMP protocol. One group of animals (mesDA RC17, green dots) wastransplanted with cells differentiated in the presence of FGF8b from day9-16 to yield caudalised VM cells of the mesencephalic dopamine (mesDA)domain. This group exhibited functional recovery as evidenced byreversal and overcompensation (by week 22) of amphetamine-inducedrotations. The other group (STN RC17, red dots) was transplanted withcells differentiated in the absence of FGF8b to yield rostral VM cellsof the STN domain. In contrast to the mesDA group, the STN group did notexhibit functional recovery of amphetamine-induced rotations.

DETAILED DESCRIPTION

A more complete understanding of the compositions and methods disclosedherein can be obtained by reference to the accompanying drawings. Thesefigures are merely schematic representations based on convenience andthe ease of demonstrating the present disclosure, and are, therefore,not intended to define or limit the scope of the exemplary embodiments.

Although specific terms are used in the following description for thesake of clarity, these terms are intended to refer only to theparticular structure of the embodiments selected for illustration in thedrawings, and are not intended to define or limit the scope of thedisclosure. In the drawings and the following description below, it isto be understood that like numeric designations refer to components oflike function.

The singular forms “a,” “an,” and “the” include plural referents unlessthe context clearly dictates otherwise.

As used in the specification and in the claims, the term “comprising”may include the embodiments “consisting of” and “consisting essentiallyof.” The terms “comprise(s),” “include(s),” “having,” “has,” “can,”“contain(s),” and variants thereof, as used herein, are intended to beopen-ended transitional phrases, terms, or words that require thepresence of the named ingredients/steps and permit the presence of otheringredients/steps. However, such description should be construed as alsodescribing compositions or processes as “consisting of” and “consistingessentially of” the enumerated ingredients/steps, which allows thepresence of only the named ingredients/steps, along with any impuritiesthat might result therefrom, and excludes other ingredients/steps.

Numerical values in the specification and claims of this applicationshould be understood to include numerical values which are the same whenreduced to the same number of significant figures and numerical valueswhich differ from the stated value by less than the experimental errorof conventional measurement technique of the type described in thepresent application to determine the value.

All ranges disclosed herein are inclusive of the recited endpoint andindependently combinable (for example, the range of “from 2 to 10” isinclusive of the endpoints, 2 and 10, and all the intermediate values).

The term “about” can be used to include any numerical value that canvary without changing the basic function of that value. When used with arange, “about” also discloses the range defined by the absolute valuesof the two endpoints, e.g. “about 2 to about 4” also discloses the range“from 2 to 4.” The term “about” may refer to plus or minus 10% of theindicated number.

Several well-known references that may be relevant to the presentdisclosure include: Molecular Cloning: A Laboratory Manual (Sambrook, etal., 1989, Cold Spring Harbor Laboratory Press), Gene ExpressionTechnology (Methods in Enzymology, Vol. 185, edited by D. Goeddel, 1991.Academic Press, San Diego, Calif.), “Guide to Protein Purification” inMethods in Enzymology (M. P. Deutshcer, ed., (1990) Academic Press,Inc.); PCR Protocols: A Guide to Methods and Applications (Innis, et al.1990. Academic Press, San Diego, Calif.), Culture of Animal Cells: AManual of Basic Technique, Second Ed. (R. I. Freshney. 1987. Liss, Inc.New York, N.Y.), Gene Transfer and Expression Protocols, pp. 109-128,ed. E. J. Murray, The Humana Press Inc., Clifton, N.J.), or the Ambion1998 Catalog (Ambion, Austin, Tex.).

As used herein, the term “laminin-521” refers to the protein formed byjoining α5, β2 and γ1 chains together. The term should be construed asencompassing both recombinant laminin-521 and heterotrimeric laminin-521from naturally occurring sources.

As used herein, the term “laminin-111” refers to the protein formed byjoining α1, β1 and γ1 chains together. The term should be construed asencompassing both recombinant laminin-111 and heterotrimeric laminin-111from naturally occurring sources.

As used herein, the term “laminin-121” refers to the protein formed byjoining α1, β2 and γ1 chains together. The term should be construed asencompassing both recombinant laminin-121 and heterotrimeric laminin-121from naturally occurring sources.

As used herein, the term “laminin-421” refers to the protein formed byjoining α4, β2 and γ1 chains together. The term should be construed asencompassing both recombinant laminin-421 and heterotrimeric laminin-421from naturally occurring sources.

As used herein, the term “laminin-511” refers to the protein formed byjoining α5, β1 and γ1 chains together. The term should be construed asencompassing both recombinant laminin-511 and heterotrimeric laminin-511from naturally occurring sources.

The term “intact” refers to the protein being composed of all of thedomains of the α-chain, β-chain, and γ-chain, with the three chainsbeing joined together to form the heterotrimeric structure. The proteinis not broken down into separate chains, fragments, or functionaldomains. The term “chain” refers to the entirety of the alpha, beta, orgamma chain of the laminin protein. The term “fragment” refers to anyprotein fragment which contains one, two, or three functional domainsthat possesses binding activity to another molecule or receptor.However, a chain should not be considered a fragment because each chainpossesses more than three such domains. Similarly, an intact lamininprotein should not be considered a fragment. Examples of functionaldomains include Domains I, II, III, IV, V, VI, and the G domain.

As used herein, the term “self-renewal” refers to the ability of thestem cell to go through numerous cycles of cell division and remainundifferentiated (i.e. pluripotent). Pluripotency itself refers to theability of the stem cell to differentiate into any cell type. The term“proliferation” refers to the ability of the stem cell to divide.Survival refers to the ability of the stem cell to live, whetherdifferentiated or undifferentiated, and does not require the stem cellto maintain its ability to divide or to differentiate.

The abbreviation “DA” refers to dopamine. It is generally used herein torefer to cells that can produce dopamine or to cells that can give riseto dopamine-producing cells.

The combination of the laminin substrate with the cell culture medium ofthe present disclosure results in a cell culture system that providesclinical grade dopaminergic cells. Particularly the method disclosesmore dopaminergic cells

The present disclosure relates to more efficient methods of culturingstem cells to obtain differentiated neural cells for regenerativetherapies. In particular, a laminin is used as a matrix/substrate forpluripotent stem cells, resulting in more differentiated cells thancultures containing alternative matrices. Only one laminin may be usedas the matrix/substrate, or the matrix/substrate can include specificlaminins, which are laminin-111 (LN-111), LN-121, LN-521, LN-421, orLN-511. Laminin-111 can normally be found in the epithelia and dermalpapillae, endothelial cells, pancreas, peripheral nerves, and placenta.

The present disclosure also relates to different cell culture mediumsthat are used to provide nutrition to cells, particularly stem cells. Inthis regard, stem cells typically require two things to be cultured: (1)a substrate or coating that provides a structural support for the stemcell; and (2) a cell culture medium to provide nutrition to the stemcell. The substrate or coating (1) is generally placed on, for example,a petri dish or some other container. Application of different cellculture mediums at appropriate time intervals in combination with alaminin-111 substrate result in a larger number of differentiated neuralcells that produce dopamine (i.e. dopaminergic cells).

The stem cells that can be used with the methods and materials disclosedherein can be induced pluripotent stem cells, embryonic stem cells,adult stem cells, fetal stem cells, amniotic stem cells, and generallyany pluripotent stem cell.

The methods can be modified to obtain neural cells of many differentphenotypes. These neural cells can be used for stem cell basedtherapies, including being transplanted and grafted into the brain of amammalian patient to treat various neurodegenerative diseases. In theabsence of patterning factors, neural cells of a telencephalic fate areobtained. Rostro-caudal and dorsal-central patterning of neuralprogenitors can be controlled by a dose-dependent addition of patterningfactors. These methods are described with reference to FIG. 2, whichprovides a timeline and a listing of the various ingredients in the cellculture mediums disclosed herein. As seen here, pluripotent stem cellsare seeded on plates coated with laminin-111 and are cultured over aperiod of 16 days. The culturing media may contain various combinationsof medium, differentiation factors, and patterning factors administeredat specific intervals over a 16-25 day period.

Initially, four different cell culture mediums are illustrated, whichare modified by the addition of differentiation factors and/orpatterning factors to arrive at multiple different cell culture mediums.Those four mediums are referred to herein as neural induction medium(NIM), N2 medium (N2M), neural proliferation medium (NPM), and B27medium (B27M).

The NIM, N2M, NPM, and B27M are made from a set of common ingredients.These common ingredients include DMEM/F12 medium, which is commerciallyavailable from Invitrogen (catalog nos. 10565 and 21331). DMEM/F12generally contains the following ingredients listed in Table 1:

TABLE 1 Concentration DMEM/F12 Ingredients (ng/mL) Glycine 187.5L-Alanine 44.5 L-Arginine hydrochloride 1475 L-Asparagine-H₂O 75L-Aspartic acid 66.5 L-Cysteine hydrochloride-H₂O 175.6 L-Cystine 2HCl312.9 L-Glutamic Acid 73.5 L-Glutamine 3650 L-Histidinehydrochloride-H₂O 314.8 L-Isoleucine 544.7 L-Leucine 590.5 L-Lysinehydrochloride 912.5 L-Methionine 172.4 L-Phenylalanine 354.8 L-Proline172.5 L-Serine 262.5 L-Threonine 534.5 L-Tryptophan 90.2 L-Tyrosinedisodium salt dihydrate 557.9 L-Valine 528.5 Biotin 0.035 Cholinechloride 89.8 D-Calcium pantothenate 22.4 Folic Acid 26.5 Niacinamide20.2 Pyridoxine hydrochloride 20 Riboflavin 2.19 Thiamine hydrochloride21.7 Vitamin B₁₂ 6.8 i-Inositol 126 Calcium Chloride (CaCl₂) (anhyd.)1166 Cupric sulfate (CuSO₄—5H₂O) 0.013 Ferric Nitrate (Fe(NO₃)₃—9H₂O)0.5 Ferric sulfate (FeSO₄—7H₂O) 4.17 Magnesium Chloride (anhydrous)286.4 Magnesium Sulfate (MgSO₄) (anhyd.) 488.4 Potassium Chloride (KCl)3118 Sodium Bicarbonate (NaHCO₃) 24380 Sodium Chloride (NaCl) 69955Sodium Phosphate dibasic 710.2 (Na₂HPO₄) anhydrous Sodium Phosphatemonobasic 625 (NaH₂PO₄—H₂O) Zinc sulfate (ZnSO₄—7H₂O) 4.32 D-Glucose(Dextrose) 31510 Hypoxanthine Na 23.9 Linoleic Acid 0.42 Lipoic Acid1.05 Phenol Red 81 Putrescine 2HCl 0.81 Sodium Pyruvate 550 Thymidine3.65

Another common ingredient is Neurobasal medium, which is commerciallyavailable as MACS neuro medium from Miltenyi (catalog no. 130-093-570)or from Life Technologies (catalog no. 13712-01). N2 supplement iscommercially available from Life Technologies (catalog no. A13707-01) in100× concentration. B27 supplement without vitamin A can be obtainedfrom Life Technologies (catalog no. 12587-010) or as MACS NeuroBrew-21from Miltenyi (catalog no. 130-097-263).

The NIM, N2M, NPM, and B27M mediums are made by mixing parts by volumeof these common ingredients with other additives.

The neural induction medium (NIM) is formed from 1 part by volume (pbv)of a 50:50 mixture of DMEM/F12: Neurobasal; 1 part of 1×N2 supplement(1:100); and 1 part of 1×B27 supplement (1:50); with addition of 2 mML-glutamine and optionally 0.2% penicillin/streptavidin if needed.

The N2 medium (N2M) is formed from 1 part by volume (pbv) of a 50:50mixture of DMEM/F12: Neurobasal; and 1 part of 1×N2 supplement; withaddition of 2 mM L-glutamine and optionally 0.2% penicillin/streptavidinif needed. In comparison to the NIM, the N2M does not contain B27supplement at all.

The neural proliferation medium (NPM) is formed from 1 part of the 50:50mixture of DMEM/F12: Neurobasal; 1 part of 0.5×N2 supplement (1:200);and optionally 1 part of 0.5×B27 supplement (1:100); with addition of 2mM L-glutamine and optionally 0.2% penicillin/streptavidin if needed.The N2 and B27 supplements are more diluted in the NPM compared to theNIM and the B27M. When B27 is present, this may be referred to as NPM-B.

The B27 medium (B27M) is formed from 1 part of Neurobasal medium; and 1part of 1×B27 supplement (1:50); with addition of 2 mM L-glutamine andoptionally 0.2% penicillin/streptavidin if needed. The B27M does notcontain N2 supplement at all.

The differentiation factors used in the present disclosure include aTGFβ inhibitor; recombinant human noggin; a brain derived neurotrophicfactor (BDNF); ascorbic acid (AA); a glial cell line-derivedneurotrophic factor (GDNF); a cyclic adenosine monophosphate (cAMP) suchas dibutyryl-cyclic adenosine monophosphate (db-cAMP); and agamma-secretase inhibitor such as DAPT. In particular embodiments, theTGFβ inhibitor is SB431542 (CAS#301836-41-9). Noggin can be obtainedfrom R&D Systems (catalog no. 6057-GMP) or Miltenyi (catalog no.130-103-456). BDNF (catalog no. 130-096-286) and GDNF (catalog no.130-098-449) can be obtained from Miltenyi.

The patterning factors used in the present disclosure include a GSK3inhibitor, fibroblast growth factor (FGF), and sonic hedgehog protein.In particular embodiments, the GSK3 inhibitor is CHIR99021(CAS#252917-06-9). In other particular embodiments, the fibroblastgrowth factor is FGF8b. In yet other embodiments, the particular sonichedgehog protein is SHH-C24II.

In particular embodiments, a ROCK inhibitor may be used for certainportions of the methods. The ROCK inhibitor may be Y27632(CAS#129830-38-2). Noggin protein and a gamma-secretase, such as DAPT,can also be used.

Next, prior to differentiation, cells may be maintained on Cellstart orlaminin-521 in StemPro medium or iPSBrew (catalog number 130-104-368).The cells may also be passaged with EDTA 4 to 6 days before initiationof differentiation. Healthy pluripotent stem cells should be used.

Referring now to FIG. 2 and FIG. 3, the differentiation protocol beginson Day 0, and continues for 16 days. After 16 days, the cells can beprepared for transplantation. On Day 0, the pluripotent stem cells areplated onto a substrate of laminin-111, LN-121, LN-521, LN-421, and/orLN-511. The substrate may consist entirely of laminin-111, entirely ofLN-121, or be a combination of LN-111 and LN-121, or a combination ofthe other named laminins as well. The substrate may also include otherbasal factors. In particular embodiments, the laminin(s) consists ofintact laminin, i.e. containing the entirety of all three chains. It isalso contemplated that the substrate could consist of fragments of thespecified laminin(s) in other particular embodiments. The stem cells canbe plated at a density of about 10,000 cells per cm².

At least two different protocols/methods for differentiating the stemcells on the laminin-coated substrate during this 16-25 day period arecontemplated herein. One protocol is illustrated in FIG. 2, and theother protocol is illustrated in FIG. 3.

In the protocol of FIG. 2, four different cell culture mediums areapplied to the stem cells. The composition of those four cell culturemediums is now described. These cell culture mediums are referred toherein as a primary cell culture medium, a secondary cell culturemedium, a tertiary cell culture medium, and a quaternary cell culturemedium.

The primary cell culture medium comprises the N2M, a TGF-β inhibitor;and a GSK3 inhibitor. No B27 supplement is present. In particularembodiments, the primary cell culture medium consists of these listedingredients. The TGF-β inhibitor is present in a concentration of about5 μM to about 15 μM, and in particular about 10 μM. In specificembodiments, the TGF-β inhibitor is SB431542. The GSK3 inhibitor ispresent in a concentration of about 0.2 μM or greater. In specificembodiments, the GSK3 inhibitor is CHIR99021. In some embodiments, theprimary cell culture medium further comprises a sonic hedgehog (SHH)protein, such as SHH-C24II. When present, the SHH protein is present inan amount of at least 50 ng/ml, including about 100 ng/ml to about 400ng/ml, and in particular about 200 ng/ml. Noggin may also be present inan amount of about 50 ng/ml to about 150 ng/ml, and in particular about100 ng/ml. Noggin also acts as a TGF-β inhibitor. In additionalparticular embodiments, the primary cell culture medium consists ofthese listed ingredients (including the SHH and the noggin). A ROCKinhibitor is present in the medium for the first 24 hours to 72 hoursafter plating. In specific embodiments the ROCK inhibitor is Y-27632.The ROCK inhibitor is present at a concentration of about 5 μM to about15 μM, and in particular about 10 μM. If desired, the primary cellculture medium containing the ROCK inhibitor (“primary-A”) can beconsidered a different medium from the primary cell culture medium thatdoes not contain the ROCK inhibitor (“primary-B”).

The secondary cell culture medium comprises the N2M and a fibroblastgrowth factor (FGF). In particular embodiments, the secondary cellculture medium consists of these listed ingredients. No B27 supplementis present. The FGF is present in an amount of about 50 ng/ml to about150 ng/ml, and in particular about 100 ng/ml. In particular embodiments,the fibroblast growth factor is FGF8b.

The tertiary cell culture medium comprises the B27M, a ROCK inhibitor, afibroblast growth factor (FGF), a brain derived neurotrophic factor(BDNF), and ascorbic acid (AA), and optionally a glial cell-line derivedneurotrophic factor (GDNF). Please note that B27 is present in thismedium, but N2 is not present. In particular embodiments, the tertiarycell culture medium consists of these listed ingredients. The FGF ispresent in an amount of about 50 ng/ml to about 150 ng/ml, and inparticular about 100 ng/ml. In particular embodiments, the fibroblastgrowth factor is FGF8b. The BDNF is present in an amount of about 5ng/ml to about 30 ng/ml, and in particular about 20 ng/ml. The AA ispresent in a concentration of about 0.1 mM to about 0.5 mM, and inparticular about 0.2 mM. The ROCK inhibitor is present in aconcentration of about 5 μM to about 15 μM, and in particular about 10μM. The GDNF can be present in an amount of about 2 ng/ml to about 20ng/ml, and in particular about 10 ng/ml, but is usually excluded.

The quaternary cell culture medium comprises the B27M, a fibroblastgrowth factor (FGF), a brain derived neurotrophic factor (BDNF), andascorbic acid (AA), and optionally a glial cell-line derivedneurotrophic factor (GDNF). Please note that B27 is present in thismedium, but N2 is not present. In particular embodiments, the quaternarycell culture medium consists of these listed ingredients. The FGF ispresent in an amount of about 50 ng/ml to about 150 ng/ml, and inparticular about 100 ng/ml. In particular embodiments, the fibroblastgrowth factor is FGF8b. The BDNF is present in an amount of about 5ng/ml to about 30 ng/ml, and in particular about 20 ng/ml. The AA ispresent in a concentration of about 0.1 mM to about 0.5 mM, and inparticular about 0.2 mM. The GDNF can be present in an amount of about 2ng/ml to about 20 ng/ml, and in particular about 10 ng/ml, but isusually excluded. The quaternary cell culture medium is generallyidentical to the tertiary cell culture medium, but does not contain ROCKinhibitor.

Next, the differentiation protocol of FIG. 2 is described. The stemcells can be plated at a density of about 10,000 cells per cm². Afterthe stem cells are originally plated on the laminin-coated substrate (asdescribed above), the primary cell culture medium is applied for aperiod of about 156 hours to about 228 hours (i.e. about 7 days to about9 days). The primary cell culture can be periodically renewed. Theprimary cell culture medium is then removed, and the secondary cellculture medium is added to the substrate.

In this regard, the secondary cell culture medium contains FGF, anddifferent amounts of the FGF and timing of the FGF addition (i.e. 7-9days) can control the rostral-caudal patterning of the resulting cells.The secondary cell culture medium is then removed about 252 hours toabout 276 hours after the original plating (i.e. about 11 days). Putanother way, the cells are exposed to the secondary cell culture mediumfor a period of about 36 hours to about 60 hours (i.e. about 2 to 4days).

The cells are then replated through dissociation to single cells, andexposed to the tertiary cell culture medium which contains the ROCKinhibitor. The cell density at replating may be about 0.5 million cellsper cm² to about 1 million cells per cm². It is contemplated that thetertiary cell culture medium is used for only a short period of time,i.e. about 48 hours or less, during the replating. The cells are thenexposed to the quaternary cell culture medium until about 324 hours toabout 396 hours (i.e. about 14-16 days) after the original plating. Putanother way, the cells are exposed to the quaternary cell culture mediumfor a period of about 108 hours to about 132 hours (i.e. about 5 days).After about 14-16 days, the cell density may be as high as about 1.78million cells per cm². After about 16 days to about 25 days, the neuralcells are ready for cryopreservation or transplantation. The identity ofthe desired cells can be verified by expression of desired markers, asdescribed further herein.

Referring now to FIG. 3, six different cell culture mediums are appliedto the stem cells and the laminin-coated substrate during this 25-dayperiod. The composition of those six cell culture mediums are nowdescribed.

The first cell culture medium comprises the NIM or the N2M; a ROCKinhibitor; a TGFβ inhibitor; and a GSK3 inhibitor. In particularembodiments, the first cell culture medium consists of these listedingredients. The various additives may be any combination of thespecific additives previously described above. The ROCK inhibitor ispresent in a concentration of about 5 μM to about 15 μM, and inparticular about 10 μM. The TGFβ inhibitor is present in a concentrationof about 5 μM to about 15 μM, and in particular about 10 μM. The GSK3inhibitor is present in a concentration of about 0.2 μM or greater. Aswill be explained further herein, the amount/concentration of the GSK3inhibitor will affect the type of neural cell that is obtained. In someembodiments, the first cell culture medium further comprises a sonichedgehog (SHH) protein. When present, the SHH protein is present in anamount of at least 50 ng/ml, including about 100 ng/ml to about 300ng/ml, and in particular about 200 ng/ml. Noggin may also be present inan amount of about 50 ng/ml to about 150 ng/ml, and in particular about100 ng/ml. Noggin also acts as a TGFβ inhibitor. In additionalparticular embodiments, the first cell culture medium consists of theselisted ingredients (including the SHH and the noggin).

The second cell culture medium comprises the NIM or the N2M; a TGFβinhibitor; and a GSK3 inhibitor; but does not contain the ROCK inhibitorthat was present in the first cell culture medium. In particularembodiments, the second cell culture medium consists of these listedingredients. The amounts of these additives are as described above. Insome embodiments, the second cell culture medium further comprises asonic hedgehog (SHH) protein. When present, the SHH protein is presentin an amount of at least 50 ng/ml, including about 100 ng/ml to about300 ng/ml, and in particular about 200 ng/ml. Noggin may also be presentin an amount of about 100 ng/ml to about 300 ng/ml in this second cellculture medium, and in particular about 200 ng/ml. In particularembodiments, the second cell culture medium consists of these listedingredients (including the SHH and the noggin).

The third cell culture medium comprises (i) the NPM or the N2M; and (ii)a TGFβ inhibitor. The TGFβ inhibitor is present in a concentration ofabout 5 μM to about 15 μM, and in particular about 10 μM. Noggin mayalso be present in an amount of about 50 ng/ml to about 150 ng/ml, andin particular about 100 ng/ml. In some embodiments, the third cellculture medium further comprises a GSK3 inhibitor and SHH protein. Whenpresent, the GSK3 inhibitor is present in a concentration of about 0.2μM or greater. When present, the SHH protein is present in an amount ofat least 50 ng/ml, including about 100 ng/ml to about 300 ng/ml, and inparticular about 200 ng/ml. In particular embodiments, the third cellculture medium consists of the NPM or N2M, TGFβ inhibitor, GSK3inhibitor, and SHH protein.

The fourth cell culture medium comprises (i) the NPM or the N2M; and(ii) a FGF. The FGF is present in an amount of about 50 ng/ml to about150 ng/ml, and in particular about 100 ng/ml.

The fifth cell culture medium comprises the B27M; a brain derivedneurotrophic factor (BDNF); ascorbic acid (AA); a glial cellline-derived neurotrophic factor (GDNF); and a FGF. In particularembodiments, the fifth cell culture medium consists of these listedingredients. The BDNF is present in an amount of about 5 ng/ml to about30 ng/ml, and in particular about 20 ng/ml. The AA is present in aconcentration of about 0.1 mM to about 0.5 mM, and in particular about0.2 mM. The GDNF is present in an amount of about 2 ng/ml to about 20ng/ml, and in particular about 10 ng/ml. The FGF is present in an amountof about 50 ng/ml to about 150 ng/ml, and in particular about 100 ng/ml.

The sixth cell culture medium can be used for neuronal maturation; andcomprises the B27M; a BDNF; ascorbic acid (AA); a GDNF; db-cAMP; and agamma-secretase. In particular embodiments, the sixth cell culturemedium consists of these listed ingredients. The BDNF is present in anamount of about 5 ng/ml to about 30 ng/ml, and in particular about 20ng/ml. The AA is present in a concentration of about 0.1 mM to about 0.5mM, and in particular about 0.2 mM. The GDNF is present in an amount ofabout 2 ng/ml to about 20 ng/ml, and in particular about 10 ng/ml. Thedb-cAMP is present in a concentration of about 200 μM to about 800 mM,and in particular about 500 μM. The gamma-secretase is present in aconcentration of about 0.1 μM to about 5 μM, and in particular about 1μM.

After the stem cells are originally plated on the laminin-coatedsubstrate, the first cell culture medium is applied for a period ofabout 36 hours to about 60 hours, and in particular for about 48 hours(i.e. 2 days). The first cell culture medium is then removed, and thesecond cell culture medium is added to the substrate. The second cellculture medium is removed about 84 hours to about 108 hours after theoriginal plating (i.e. about day 4), and is replaced with the third cellculture medium. The third cell culture medium can be renewed about 156hours to about 180 hours after the original plating. The third cellculture medium is then removed about 156 hours to about 228 hours afterthe original plating (i.e. about 7-9 days after original plating).

In this regard, rostro-caudal patterning of the resulting cells can becontrolled by dose-dependent addition of the GSK3 inhibitor during thisinitial period using the first through third cell culture mediums. Insome embodiments, 0.2 μM to 0.4 μM of the GSK3 inhibitor are used inthese cell culture mediums for diencephalic fates. In other embodiments,0.6 μM to 0.8 μM of the GSK3 inhibitor may be used for mesencephalicfates. In yet other embodiments, 1 μM to 2 μM of the GSK3 inhibitor maybe used for anterior rhomencephalic fates. In yet further embodimentsmore than 4 μM of the GSK3 inhibitor may be used for posteriorrhomencephalic fates.

Similarly, dorso-ventral patterning of neural progenitors can becontrolled by dose-dependent addition of the SHH protein. In someembodiments, if no SHH protein is added to the culture, the cells willbe enriched for alar plate fates. In other embodiments, about 50 ng/mlto about 150 ng/mL SHH protein may be added to enrich for basal platefates. In yet other embodiments, more than 200 ng/mL SHH protein may beadded to enrich for floor plate fates. To enrich for roof plate fates,no TGFβ inhibitor or noggin should be present in the third cell culturemedium (applied about Day 4). This allows for activation of bonemorphogenic protein (BMP).

In some embodiments, purmorphamine and SHH protein may be added to thesecond and third cell culture mediums to obtain more potentventralization. The purmorphamine should be present in a concentrationof about 0.1 μM to about 1 μM, and in particular about 0.5 mM.

Continuing on, the third cell culture medium is substituted with thefourth cell culture medium after about 156 hours to about 228 hoursafter the original plating. As discussed above, the amount and timing ofthe FGF in the fourth cell culture medium can control rostral-caudalpatterning of the progenitor cells. The fourth cell culture medium isthen removed about 252 hours to about 276 hours after the originalplating (i.e. about 11 days after original plating). At this time, thecells may be replated on a second laminin-coated substrate, and thefifth cell culture medium is applied. The cells are cultured in thefifth cell culture medium until about 324 hours to about 396 hours afterthe original plating (i.e. about day 14-16). The fifth cell culturemedium may be renewed about 324 hours to about 348 hours after theoriginal plating as well.

After about 14-16 days, the identity of the cells of these processesusing the first through fifth cell culture mediums can be verified byexpression of regional markers including FOXG1, OTX2, LMX1A, FOXA2, andHOXA2. After about 16 days to about 25 days, the neural cells are readyfor cryopreservation or transplantation. If the cells are being used forlonger-term studies that need mature neuronal phenotypes, they can becultured in the sixth cell culture medium. The resulting neural cellsare obtained in a large quantity.

The cell culture media of FIG. 2 and FIG. 3 can be compared to eachother. The primary cell culture medium of FIG. 2 is similar to thesecond cell culture medium of FIG. 3. The secondary cell culture mediumof FIG. 2 is similar to the fourth cell culture medium of FIG. 3. Thequaternary cell culture medium of FIG. 2 (B27M) is similar to the fifthcell culture medium of FIG. 3 (NDM).

The following examples are for purposes of further illustrating thepresent disclosure. The examples are merely illustrative and are notintended to limit devices made in accordance with the disclosure to thematerials, conditions, or process parameters set forth therein.

EXAMPLES Coating Plates with Laminin-111

Prior to initiating differentiation, about 1 μg/cm² Laminin-111 in PBSand Ca²⁺/Mg²⁺ (total volume 300 μL) was coated onto a 24 well plate. Fora few wells, laminin-111 and PBS were mixed directly into the wells. Theplate was shaken to ensure homogenous coating. The plate was thencovered with parafilm and left at 4° C. for about 1 to about 7 daysbefore use.

Dilution of CHIR99021

10 mM CHIR99021 stock in DMSO was prepared. The stock was distributedbetween aliquots (5-10 μL per vial) and stored at −20° C. The aliquotscan be thawed up to three times before discarding.

For use in culturing, CHIR99021 was diluted 1:100 in N2M to yield a 100μM solution prior to adding to the cell culture medium.

Example 1 Materials and Methods

Neural induction medium (NIM), Y-27632 (10 μM), SB431542 (10 μM) andnoggin (100 ng/mL) were combined to create a differentiation medium.Approximately 250 μL of medium was needed per cm² of differentiation.For patterning to ventral mesencephalic fates, 0.6 to 1.0 μM CHIR99021and 200 ng/mL Shh-C24II was added to the medium.

Colonies appeared pluripotent and any differentiated colonies wereremoved from the culture before initiating differentiation. StemMACSiPSBrew medium was aspirated and cells washed once in PBS. EDTA (0.5 mM)was added to the cells and the cells incubated at room temperature forabout 7 minutes. The plate was rocked occasionally to ensure the cellswere submerged in EDTA.

10 mL wash medium (DMEM/F12 with 0.1% albumin or other medium similar togrowth medium) was prepared in a 15 mL tube. EDTA was removed and 1 mLwash medium was transferred to the plate.

Colonies were immediately pipetted off the dish with a pipette andtriturated to yield homogenous sizes while avoiding dissociation tosingle cells. The colonies were then transferred to the 15 mL tube withthe wash medium. The cell suspension was mixed and 1 mL suspension wastransferred to a 1.5 mL tube for counting. The tube was spun at 400×gfor 5 minutes.

Medium from the 1.5 mL tube was aspirated and cells resuspended in 100μL accutase. The cells were left in an incubator for 7 minutes to yielda single cell suspension. 900 μL wash medium was added to the 1.5 mLtube and cells dissociated with the pipette. Cells were then counted toestimate the total number of cells in suspension. Approximately 10,000cells/cm² were required to initiate differentiation and transferred fromsuspension to a new tube before being spun down at 400×g for 5 minutes.

The wash medium was aspirated and re-suspended in a mixeddifferentiation medium of NIM, Y-27632 (10 μM), SB431542 (10 μM), noggin(100 ng/ml), CHIR99021 (0.7 μM) and SHH-C24II (200 ng/ml) to yield acell suspension of 50,000 cells/mL. Laminin-111 was aspirated from thecoated plate and the cell suspension seeded onto the coated plate with10,000 cells/cm² (approximately 250 μL medium per cm²). The plate wasthoroughly shaken and swirled to yield homogenous cell plating.

After about 48 hours (Day 2), the medium was changed to new neuralinduction medium (NIM) with SB431542 (10 μM) and noggin (100 ng/mL). Forpatterning to ventral mesencephalic fates, 0.6 to 1.0 μM CHIR99021 and200 ng/mL SHH-C24II were added to the medium. The same volume ofdifferentiation medium was used as the volume used to initiatedifferentiation.

After about 48 hours (i.e., about 96 hours from plating, Day 4), themedium was changed to neural proliferation medium (NPM) with SB431542(10 μM) and noggin (100 ng/mL). For patterning to ventral mesencephalicfates, 0.6 to 1.0 μM CHIR99021 and 200 ng/mL Shh-C24II were added to themedium. Approximately 350 μL medium was added per cm².

After about 72 hours (i.e., about 168 hours from plating, Day 7), themedium was refreshed with NPM with SB431542 (10 μM) and noggin (100ng/mL). For patterning to ventral mesencephalic fates, 0.6 to 1.0 μMCHIR99021 and 200 ng/mL Shh-C24II were added to the medium.Approximately 350 μL medium was added per cm².

After about 48 hours (i.e., about 216 hours from plating, Day 9), themedium was changed to NPM with fibroblast growth factor (FGF8b) (100ng/mL). Approximately 500 μL medium was added per cm².

After about 48 hours (i.e., about 264 hours from plating, Day 11), thecells were replated onto a new 12 well laminin-111 coated plate. Cellswere washed twice with PBS and shaken in the plate to remove all deadand floating cells. Approximately 300 μL accutase was added to eachwell. Cells were left in the incubator for 10 minutes and rockedoccasionally to ensure that the cells were submerged in accutase.

A 15 mL tube was prepared with 10 mL NPM. After 10 minutes, the cellswere dissociated with a 1 mL pipette to yield a single cell suspensionand transferred to the 15 mL tube containing NPM. Cells were spun downat 400×g for 5 minutes. The medium was then aspirated and the cellpellet transferred and resuspended in 1 mL NPM in a 1.5 mL tube. 10 μLcell suspension was removed for counting. The suspension was diluted1:10-1:50. While counting, cells were spun down at 400×g for 5 minutes.

The medium was aspirated and cells resuspended to a density of 1.7million cells/mL in B27 medium (B27M), brain derived neurotrophic factor(BDNF) (20 ng/mL), ascorbic acid (AA) (0.2 mM), glial cell line-derivedneurotrophic factor (GDNF) (10 ng/mL) and FGF8b (100 ng/mL). Laminin-111was aspirated from the coated plates and cells seeded onto the plate ata density of 800,000 cells/cm². The plate was thoroughly shaken andswirled to yield homogenous plating of the cells before incubation.

After 72 hours (i.e., about 336 hours after plating, Day 14), medium onthe cells was refreshed with B27M, BDNF (20 ng/mL), AA (0.2 mM), GDNF(10 ng/mL), and FGF8b (100 ng/mL). Approximately 500 μL medium was addedper cm².

After 48 hours (i.e., about 384 hours after plating, Day 16), the cellswere ready for cryopreservation and/or transplantation.

Validation of Progenitor Cell Phenotype

Parallel plates of cells were kept in B27M with BDNF, ascorbic acid, andFGF8b until day 14 (i.e. 336 hours after plating) and then harvested forRNA analysis or fixed for immunocytochemistry. On day 14, the regionalidentities of the cells were clearly identified by their expressions ofregional markers such as FOXG1, OTX2, LMX1A, FOXA2, and HOXA2.

Example 2 Materials and Methods

The same materials and protocol disclosed in Example 1 are used for 24well plates with the following alterations:

Plates were coated with laminin-111 (1 μg/cm²) in PBS and Ca²⁺/Mg²⁺ (700μL/cm²). For seeding the cell suspension onto the laminin-111 coatedplates, approximately 250 μL was required per cm² (500 μL/well). Toinitiate differentiation, for 6 wells of a 24 well plate, 120,000 cellsin total were needed.

At the 96 hour and 168 hour marks after plating, approximately 600 μLmedium was added to each well. At the 216 hour mark after plating,approximately 700 μL medium was added to each well.

Some cell lines required the addition of 10 μM Y-27632 to the medium tosurvive replating. During replating, approximately 150 μL accutase wasadded to each well. At the 336 hour mark, approximately 700 μL mediumwas added per well.

Example 3 Preparation of Cells for Transplantation (Day 16-25)

The same materials and protocol disclosed in Examples 1 and 2 are used.

Cells were maintained in B27M, BAG (BDNF+AA+GDNF), and FGF8b until theday of transplantation without any further manipulations. Medium wasrefreshed every 2-3 days. Cells were most suitable for transplantationon day 16 but could be transplanted up until day 26. Cells fortransplantation did not receive DAPT or db-cAMP in the medium, as thiswould result in premature neuronal maturation and increased cell deathupon dissociation.

Example 4 Long-Term Terminal Neuronal Maturation

The same materials and protocol disclosed in Examples 1 and 2 are used.

Cells for long-term studies of mature neuronal phenotype were replatedagain between days 16 and 25 to avoid too high densities of cultures anddetachment of cells. Cells were kept in B27M and BAG (without db-cAMPand DAPT) until the day of replating. Replating was performed using thesame procedure as used on Day 11 (i.e., 264 hours after first plating),and cells were kept in B27M, BDNF (20 ng/mL), GDNF (10 ng/mL), ascorbicacid (0.2 mM), db-cAMP (500 μM), and DAPT (1 μM) after replating.

Replating at later timepoints should be avoided due to stress on matureneuronal cells. At late stages of differentiation, neurons may begin todetach from the plate. This can be attenuated by adding laminin andfibronectin (FN) to the cell culture medium. Mature dopaminergicphenotypes only start to appear from Day 45 and onwards.

Example 5

Over the past 6 years, over 500 rats were intracerebrally transplantedwith 31 different batches of hES cell-derived mesDA progenitors atvarious different research sites. An overview of the graft experimentplan is reflected in Tables 2-3 below. For graft site: Str.=striatum,SN=substantia nigra. For rat host strain, SD=Sprague-Dawley,LH=Lister-hooded, At=Athymic Crl:NIH-Foxnlrnu. For immunosuppression,Ciclo=daily intraperitoneal injections of ciclosporin (10 mg/kg),starting the day before transplantation.

TABLE 2 # Avg. Yield Batch Graft Animals Graft Rat host Immuno- Grafted(TH + cells/ # Survival (n_(analysed)/n_(grafted)) Site strainsuppression Cells 100,000 grafted) 1 6 weeks 7/7 Str. SD Ciclo 3 × 10⁵3711 2 6 weeks 8/8 Str. SD Ciclo 3 × 10⁵ 4616 3 6 weeks 7/7 Str. SDCiclo 3 × 10⁵ 8660 4 6 weeks 7/7 Str. SD Ciclo 3 × 10⁵ 5597 5 8 weeks 7/10 Str. SD Ciclo 3 × 10⁵ 19876 6 24 weeks 6/6 Str. AT — 3 × 10⁵ 92607 16 weeks 14/15 Str. LH Ciclo 3 × 10⁵ 273 8 24 weeks 4/9 SN AT — 1 ×10⁵ 38 11 24 weeks  9/16 Str. LH Ciclo 3 × 10⁵ 266 12 24 weeks 8/8 SN AT— 1 × 10⁵ 4007 13 A: 6 weeks 3/4 Str. SD Ciclo 2 × 10⁵ 212 B: 6 weeks3/4 Str. SD Ciclo 2 × 10⁵ 176 14 6 weeks 5/6 Str. SD Ciclo 2 × 10⁵ 17016 6 weeks 4/4 Str. SD Ciclo 1.5 × 10⁵  1052 17 24 weeks 10/10 Str. AT —3 × 10⁵ 2198 18 A: 4 weeks 4/4 Str. SD Ciclo 3 × 10⁵ 581 B: 16 weeks 5/8Str. SD Ciclo 3 × 10⁵ 1011 19 A: 4 weeks 3/4 Str. SD Ciclo 3 × 10⁵ 36 B:16 weeks 7/8 Str. SD Ciclo 3 × 10⁵ 261 20 6 weeks 4/4 Str. SD Ciclo 1.5× 10⁵  755 21 6 weeks 4/4 Str. SD Ciclo 1.5 × 10⁵  13 22 A: 18 weeks 4/4Str. SD Ciclo 2 × 10⁵ 6868 B: 24 weeks 6/6 Str. AT — 3 × 10⁵ 5822 23 A:18 weeks 3/4 Str. SD Ciclo 2 × 10⁵ 4141 B: 24 weeks 5/5 Str. AT — 3 ×10⁵ 3549 24 6 weeks 2/2 Str. SD Ciclo 4 × 10⁵ 9 25 18 weeks 4/4 Str. SDCiclo 4 × 10⁵ 7.5 26 16 weeks 5/7 Str. SD Ciclo 2.4 × 10⁵  963 27 16weeks 5/8 Str. SD Ciclo 2.4 × 10⁵  3970 28 16 weeks 3/7 Str. SD Ciclo2.4 × 10⁵  1117 29 18 weeks 5/5 Str. SD Ciclo 1.5 × 10⁵  7054 30 18weeks 4/4 SN SD Ciclo 0.75 × 10⁵   4484 31 20 weeks 9/9 Str. LH Ciclo3.4 × 10⁵  5200

TABLE 3 Avg. Vol./ Avg. TH+/ Included in 100,000 Vol. Included in FIG.7D Included Batch # (mm³) (mm³) DeSeq2 + PCA and 7E in FIG. 6G 1 10083790 DA-high 2 1141 3972 DA-high 3 2394 3579 DA-high 4 1366 4001 DA-high5 4413 4479 6 2897 3335 DA-high 7 0074 2861 DA-low 8 ND ND X X 11 01182425 DA-low 12 ND ND 13 0074 2485 DA-low 0054 1583 DA-low 14 0049 4080DA-low 16 1606 658 X 17 0537 7387 DA-high X 18 0085 5936 DA-low X X 01445894 DA-low X 19 0028 923 DA-low X X 0057 4772 DA-low X 20 0294 3791 X21 0026 527 22 1380 3573 X X 1820 3536 X X 23 0872 4754 DA-high X 08813999 DA-high 24 0043 345 DA-low X 25 0016 580 DA-low X 26 0856 1822 X 270828 4461 DA-high X 28 0208 4869 X 29 1640 4509 DA-high X X 30 1532 2911DA-high X X 31 1430 3787 X

In all experiments, the scheme of which is illustrated in FIG. 4E, hESCswere differentiated for 16 days in vitro, and various different batchesof ventral mesencephalic-patterned hESCs were grafted into ratssubjected to unilateral dopaminergic lesions with 6-OHDA. FIG. 4A is setof photographs of the grafts after the cells matured in vivo, and thebrains were stained with TH. Although all ventralmesencephalon-patterned cell batches were routinely assessed for highexpression of ventral mesencephalon markers LMX1A, FOXA2, and OTX2 priorto grating, the in vivo outcome with respect to graft size and number ofdopamine neurons varied between experiments.

To determine the level of batch-to-batch variability from theseexperiments, the total number of TH+ neurons of each animal per 100,000cells grafted (DA yield) was quantified, which is graphicallyillustrated in FIG. 4B, and the graft size was based on HuNu+ cellvolume (mm³) following immunostaining. The graphical representation ofgraft volume is seen in FIG. 4C. For all quantifications, values werereported per 100,000 cells grafted. This permitted estimation of DAdensities (TH+/mm³) for all grafts, which are represented in FIG. 4D.These quantitative assessments revealed considerable inter-experimentalvariability.

To determine what degree commonly used mesDA progenitor marks in vitropredicted TH+ content in grafts after maturation in vivo, RNA sampleswere collected from each individual cell batch enumerated above (allcontaining high levels of FOXA2/LMX1A co-expressing cells) at the day oftransplantation and analyzed. RNA samples from the same cells replatedwere also analyzed after further in vitro maturation.

FIG. 4F is a set of graphs indicating the mean TH+ cell content in eachgraft experiment plotted versus gene expression of FOXA2, LMX1A, andCORIN in the transplanted cell population on day 16 (i.e. day oftransplantation). Similarly, FIG. 4G is also a set of graphsrepresenting transplanted cell population on day 16, but the graphsindicate the gene expression of TH, NURR1, and AADC. Results from aSpearman correlation (ventral mesencephalon cells only) are given as Rand p-values in each graph, and the tendencies of correlation are shownby linear regression lines.

It was found that expression of commonly used mesDA markers FOXA2,LMX1A, and CORIN was required for dopaminergic differentiation of thegrafts. However, FOXA2 and LMX1A expression levels at the time-point oftransplantation did not correlate significantly with DA yield in thegrafts, suggesting that within the FOXA2/LMX1A co-expressing cells,additional markers are needed to predict the in vivo outcome.

FIGS. 4F and 4G represent an assessment of whether extended in vitromaturation of the progenitors into neurons reflected their correspondingin vivo maturation in the grafts. In further experiments where the cellsused for grafting had also been subjected to parallel terminaldifferentiation in vitro for 39-45 days (instead of only 16 days), itwas found that the expression levels of DA markers TH, NURR1, and AADCdid not show any statistically significant correlation to DA yield aftertransplantation.

Example 6

To enable an unbiased search for potential markers which correlatepositively with DA yield after transplantation (i.e. successful graftoutcome), global gene expression profiling was performed of cell samplescollected at the day of transplantation using RNA sequencing.

For unbiased gene expression analysis, graft experiments were dividedinto DA-high and DA-low groups based on the total number of TH+ cells inthe grafts. A graphical comparison of the TH+ content between batches isshown in FIG. 5A. Dopaminergic function of the grafts was assessed ingrafts with longterm maturation (i.e. longer than 16 weeks) throughamphetamine induced rotation or PET imaging. A “−” symbol indicates alack of functional recovery, a “+” symbol indicates functional recovery,and “ND” indicates not determined.

Importantly, all longterm grafts with lack of functional recovery werelocated in the DA-low group, whereas the DA-high group contained cellswith therapeutic potential able to mediate functional recovery.

To see if the DA-high and DA-low cell batches could be identified bydistinct gene expression profiles, an unbiased principal componentanalysis (PCA) was performed on all the selected day 16 RNA sequencingsamples. As shown in FIG. 5B, a clustering of the DA-high samples wasobserved positive PC1 axis, which contained genes such as FGF8, PAX5,EN2, and CNPY1, all of which have been shown to be important formidbrain-hindbrain boundary (MHB) formation.

As there were clearly distinct expression profiles between the twogroups, a Deseq2 analysis was conducted to identify all differentiallyexpressed genes between the DA-high and DA-low samples. FIG. 5I is agraphical analysis of predictive markers following the Deseq2 analysisof RNA sequencing data from DA-high and DA-low cell samples. Markerswere plotted based on log 2 fold change compared to mean of normalizedcounts. From the top 12 ranked genes appearing from this analysis, againa high representation was found of genes expressed in the caudal ventralmesencephalon and MHB regions to be positively associated with DA yieldin vivo, i.e. PAX5, FGF8, SPRY1, EN1, EN2, SPS, ETV4, CNPY1, TLE4, andETV5. These expression profiles are reflected in FIG. 5C. These 12 genesare those with the highest fold change and with a p-value of <0.001.

To assess the predictive value of these selected markers, a directSpearman correlation analysis was conducted between graft outcomes (i.e.TH+ content) to the RNA expression levels of selected genes from the PCAand Deseq2 analyses. FIGS. 5D-5E specifically show the results from theSpearman correlation analysis for EN1 and PAX8. Results from theSpearman correlation analysis were given as R and p-values, andcorrelations were visualized with linear regression lines. To validatethe RNA sequencing dataset, a subset of gene correlations was assessedusing qRT-PCR, including 4 additional graft experiments, which arerepresented as FIG. 5E specifically.

A summary of the RNA sequencing correlation analysis between TH+content, graft volume, and DA density and RNA levels of MHB genes andcommon ventral mesencephalon markers is shown in FIG. 5F. The schematiconly shows positive correlations defined by the Spearman correlationanalysis with p<0.05. Genes verified by qRT-PCR are shown in bold.

These correlations were compared to the correlations of commonly usedventral mesencephalon markers (i.e., LMX1A, LMX1B, FOXA2, FOXP2, CORIN,and OTX2).

The analyses showed that most of the caudal ventral mesencephalonmarkers identified by DeSeq2 showed positive correlation with graft sizeand total TH content of the grafts, as shown in FIG. 5G. FIG. 5G inparticular is a graphical representation of a Spearman distance analysisof RNA levels in cell batches, showing co-regulation of MHB genes.Markers EN1, SPRY1, WNT1, ETV5, and CNPY1 correlated positively with DAdensity (TH+/mm³). These contrasted to the broader and more widelyexpressed ventral mesencephalon markers FOXA2, LMX1A, CORIN, FOXP1, andFOXP2, which by several analyses showed negative correlations to bothgraft size and total DA yield, indicating they may be uncoupled ornegatively coupled to the MHB genes cluster. LMX1A and OTX2 showedpositive correlations only to DA density but not to DA yield of thegrafts.

To investigate whether the genes identified in the RNA sequencinganalysis formed part of a co-regulated gene network, a Spearmancorrelation analysis was performed of the expression values for eachcandidate gene towards others in 29 batches of ventralmesencephalon-patterned cells. As seen in FIG. 5G, all of the MHB genesassociated with high DA yield showed a pattern of co-regulation. Inparticular, the MHB markers SPRY1 and ETV4/5 and the caudal ventralmesencephalon markers EN1 and CNPY1 clustered in the analysis,suggesting a strong co-regulation between the genes. However, LMX1A andOTX2 showed little or no positive co-regulation with these genes. CORIN,LMX1B, FOXA2, and FOXP2 were negatively correlated with several of thecaudal genes, indicating that these commonly used markers are notspecifically associated with a caudal ventral mesencephalon phenotypeand that they may be expressed at higher levels in the more rostraldomains of the ventral mesencephalon. Other ventral mesencephalonmarkers reported to be involved in mesDA neurogenesis, namely MSX1,SOX6, and PBX1, did not show any correlations to DA density of thegrafts when analyzed in d16 ventral mesencephalon-patterned progenitors.FIG. 5H is a set of five representative images of TH+ neurons fromdifferent cell batches with high expression of predictive markers,revealing the mature morphology of the grafted cells.

Example 7

Using RNA sequencing expression values, a strong negative correlationwas found between the diencephalic markers FEZF1, WNT7B, and EPHA3 andDA yield in grafts at day 16, as shown in FIG. 6A. This correlation ledto an investigation of whether some batches of ventralmesencephalon-patterned hESCs contained BARHL1⁺ and PITX2⁺ STNprogenitors were derived from the anterior LMX1A⁺/FOXA2⁺ domain.

Both BARHL1⁺ and PITX2⁺ were detected in the differentiated cell batcheson day 16. FIG. 6B is a set of images following immunostaining ofventral mesencephalic-patterned hES cell cultures at day 16, revealingthe presence of STN domain fates (i.e. BARHL1⁺/FOXA2⁺ and PITX2⁺/LMX1⁺cells). FIG. 6C is a schematic overview of expression domains of PITX2and BARHL1 in the diencephalic STN region and in lateral midbraindomains. FIG. 6G shows the cell cultures of FIG. 6B at day 42 ofdifferentiation.

As depicted in FIGS. 6B-6C, the BARHL1⁺ cells could have been eitherFOXA2⁺ or FOXA2⁻, indicating the presence of both diencephalicfloorplate cells as well as lateral cell populations in thedifferentiated progenitor batches. It was further found thatFOXA2⁺/BARHL1⁺/MAP2⁺ neurons and PITX2⁺/LMX1A/B⁺ cells were present inthe terminally differentiated hES cell cultures, indicating thedifferentiation of these progenitors into STN fates.

FIG. 6D is a set of images following confocal imaging of 18 week oldgrafts. In animals grafted with ventral mesencephalon-patterned cells,variable presence of BARHL1⁺ cells was detected, and these cells wouldhave been either PITX2⁺ (indicating ventral diencephalic STN fates) orPITX2⁻ (indicating other lateral fates). Example images of BARHL1⁺ cellcontent in grafts derived from cell batches with low or high BARHL1 RNAlevels at the day of transplantation are shown in FIG. 6E.

To investigate if these markers could be used to predict the amount ofnon-dopaminergic lateral and rostro-ventral contaminating cells in thegrafts, the numbers of BARHL1⁺ cells were quantified in several of thegraft experiments. Correlation analysis showed that the density ofBARHL1⁺ cells in the grafts positively correlated with the expressionlevels of BARHL1 and BARHL2 in vitro in the differentiated cell batchesat the day of transplantation, as shown in FIGS. 6D and 6F. Results fromthe Spearman correlation analysis are given as R and p-values in eachgraph, and correlations are visualized with linear regression lines.

These results implied that BARHL1 and BARHL2 in progenitor culturescould be used as markers for identifying and quantifying severalcommonly occurring contaminating populations in ventralmesencephalon-patterned hESCs both in vitro and in vivo.

Example 8

Given the variable outcome of ventral mesencephalon-patterned hES cellprogenitors, it was next investigated if the patterning indifferentiation protocol could be optimized toward the caudaldopaminergic domain of the ventral mesencephalon (because markers ofthis domain correlated with high DA yield in vivo). Cells located in thecaudal ventral mesencephalon are in proximity to the MHB, and studies inthe mouse and chick models have shown that the development of mesDAprogenitors in this region depends on the activity of FGF8, a growthfactor that is secreted from the MHB. In addition, high expression ofFGF8 was found to correlate to the DA-high group in the gene expressionanalyses as seen in FIG. 5C above.

FIG. 7A is a set of graphs created following a qRT-PCR analysis at day10 of differentiating hESCs treated with exogenous FGF8b during ventralmesencephalon patterning from days 0-9. The analysis shows induction offorebrain and hindbrain markers in ventral diencephalic (CHIR=0.4 μM) orventral mesencephalic (CHIR=0.8 μM) cultures.

It was found that the addition of FGF8b to the differentiation mediumtogether with SHH and GSK3i to activate canonical WNT signaling duringthe early phase of neural induction and patterning (day 0-9) inducedsignificant upregulation of forebrain markers FOXG1 and SIX3 indiencephalic-patterned cultures and of hindbrain markers HOXA2 and GBX2in mesencephalic-patterned cultures. This indicated that earlypatterning with FGF8b caused contamination of cultures with severalnon-ventral mesencephalon progenitor fates. FIG. 7B is a set of imagesfollowing immunostaining at day 16, revealing patches of PITX2⁺ andNKX2.1⁺ cells and patches of LMX1A− cells in cultures treated with FGF8bfrom days 0-9.

In contrast, the FOXA2⁺/LMX1A⁺ phenotype of the cells was maintained, asshown in FIG. 7C, if FGF8b was added to the cells after initialpatterning towards ventral mesencephalon was completed (from day 7-16 or9-16).

FIGS. 7D-7F correspond to day 16 cultures treated with FGF8b. Theaddition of 100 ng/mL FGF8b caused caudalisation of the ventralmesencephalon progenitors when the cultures were treated with FGF8b fromday 9-16. As shown in the immunostaining images of FIG. 7D-7E, theresults of which were quantified in FIG. 7F, BARHL1⁺ and PITX2⁺ levelswere both decreased. However, whereas control ventral mesencephaloncultures were completely devoid of EN1 expression, EN1⁺ progenitors andEN1 mRNA were abundant in cultures treated with FGF8b from day 9-16.FIG. 7E is a set of images showing the immunostaining of EN1, while FIG.7G graphically represents mRNA levels of FOXA2, LMX1A, OTX2, and EN1following qRT-PCR analysis.

In summation, treatment with FGF8b from day 9-16 further caused asignificant decrease in the percentage of BARHL1+/FOXA2+ and PITX2+ STNprogenitors, which is illustrated in FIGS. 7D-7F. This decreaseindicated that late addition of FGF8b to cultures shifted progenitorfates from anterior ventral mesencephalon and STN fates toward caudalventral mesencephalon mesDA progenitor fates.

Flow cytometry analysis, exhibited as FACS plots in FIGS. 7H-7I, showedthat although addition of FGF8b from day 9-16 did not affect thepercentage of FOXA2⁺ progenitors, there was a 47% decrease in the numberof CORIN⁺ progenitors. This was in accordance with the negativecorrelations found for CORIN in the RNA sequencing analyses associatedwith FIGS. 5F-5G and indicates that CORIN expression both at the proteinand mRNA level is more strongly associated with a rostral ventralmesencephalic/diencephalic fate rather than a caudal mesDA progenitorfate.

Example 9

To develop a GMP-compatible differentiation protocol for high andreproducible yield of caudilised mesDA ventral mesencephalon progenitorsthat would result in good graft outcome, a fully GMP-derived hES cellline RC17 from Roslin cells (hPS Creg #RCe021-A) was used. Previousresearch grade ventral mesencephalon differentiation protocols haveimplemented steps of embryoid body (EB) formation or culturing onMatrigel, both of which pose problems in GMP adaptation due todifficulties in reproducibility and the content of undefinedanimal-derived component, respectively.

Seven different full-length laminin subtypes were tested, and it wasfound that four of them (LN-111, LN-421, LN-511, and LN-521) efficientlysupported adherent differentiation of ventral mesencephalon progenitorsfrom day 0-11 of the protocol. This is illustrated in FIG. 8A, which isa set of images revealing the best attachment and yield of neural cellsacross the seven tested laminin subtypes. Relative to a standard yieldof 100%, LN-111 yielded 170%, LN-421 yielded 294%, LN-511 yielded 223%,and LN-521 yielded 208%. RC17 cells were differentiated according to themethods described herein, but on plates that were coated withlaminin-121 instead of laminin-111. FIG. 8C compares the yields, and theyields are about equal to each other, i.e. LN-121 works about as well asLN-111 as a substrate.

In contrast to LN-511 and LN-521, which efficiently support growth ofhPSCs, it was found that when undifferentiated hESCs were plated ontoLN-111 in pluripotency medium (iPS brew), the cells formed spheres after4 days of culturing, that easily detached from the culture dish, asshown in the images of FIG. 8B. When the same number of cells was platedonto LN-111 in B27 medium, the cultures remained adherent and grew toconfluency after 7 days of differentiation while showing rapiddownregulation of pluripotency markers. FIG. 8D is a set of images takenat Days 0, 2, 4, and 7, exhibiting the seeding of low density hESCs onLN-111 matrix in B27 medium resulted in confluent neuralized cultures,while FIG. 8E is a graphical illustration of the pluripotency markers'mRNA levels decreasing over three days of differentiation. Thisindicated that LN-111 selectively supported the growth of neural cellsbut not pluripotent stem cells, which is in agreement with its broadexpression in the developing brain.

Next, different combinations of GMP-compatible basal medium was testedwith the aim of optimizing the total yield and purity of ventralmesencephalon progenitors. It was found that the differentiation in abasal medium of NeuroBasal+DMEM/F12 with N2 supplement but without B27supplement from day 0-11 produced the highest yield of cells on day 11.FIG. 8F is a graphical representation of the cell yield across thedifferent media.

To ensure accurate caudalisation of the ventral mesencephalonprogenitors, 100 ng/mL of FGF8b was added to the cells from day 9-16 ofdifferentiation. For full GMP compatibility, all growth factors andchemicals in the protocol were switched to those enumerated in Table 4below.

TABLE 4 Reagent Supplier Cat. No. For Differentiation iPS brew Miltenyi130-104-368 LN-521 BioLamina LN-521 LN-511 BioLamina LN-111 DPBS + Ca +Mg (CTS) LT A12858-01 EDTA LT 15575-020 PBS −/− CTS LT A12856-01DMEM:F12 LT 21331-020 Neurobasal CTS LT A13712-01 N2 supplement CTS LTA13707-01 B27 supplement w/o vitamin A LT 12587-010 L Glutamine LT25030-081 AccutaseGMP Innov. Cell Tech AccutaseGMP SB431542 Miltenyi130-105-336 CHIR99021 in 10 mM solution Miltenyi 130-106-539 Y-27632dihydrochloride Miltenyi 130-103-922 Noggin GMP R&D 6057-GMP BDNF GMPR&D 248-GMP SHH C24II premium grade Miltenyi 130-095-727 Ascorbic acidTocris 4055 FGF8b premium grade Miltenyi 130-095-740 For TransplantationHBSS (no Ca/Mg, no phenol red) LT 14175-046 Pulmozyme (dornase alpha)Roche 11899

As illustrated in FIG. 2, the GMP-compatible protocol consisted ofplating approximately 1×10⁶ hESCs on a substrate containing LN-111,which were then cultured with N2 medium, SB431542, Noggin, Shh-C24II,and CHIR 99021 on days 0-9. The first culture was then removed and theplated cells were exposed to N2 medium and FGF8b on days 9-11, resultingin progenitors. The progenitor cells were then replated onto threeseparate plates at 0.8×10⁶/cm² with a ROCK inhibitor (Y-27632). On days11-16, the Y-27632 was removed and each plate was cultured in B27,FGF8b, BDNF, and ascorbic acid to result in cells covering an area ofapproximately 1.78±0.13×10⁶/cm³. This final yield was more than 40 timeshigher than the yield obtained with the original EB-based research gradedifferentiation protocol.

Based on these numbers, it was extrapolated that more than 380 milliontransplantable progenitor cells could be produced in 16 days whenstarting from 1 million undifferentiated hESCs. FIG. 8G is a graphicalillustration of the counted cells from the EB-based protocol compared tothe counted cells from the GMP/LN-111 protocol.

After terminally differentiating these progenitors in vitro, patch-clampelectrophysiology was performed on hESC differentiated to a ventralmesencephalon fate at day 45 post-differentiation. Cells grown oncoverslips were submerged in a continuously flowing Krebs solution (119mM NaCl, 2.5 mM KCl, 1.3 mM MgSO₄, 2.5 mM CaCl₂, 25 mM Glucose and 26 mMNaHCO₃) gassed with 95% O₂-5% CO₂ at 28° C. Recordings were made with aMulticlamp 700B amplifier (Molecular Devices), using borosilicate glasspipettes (3-7 MOhm) filled with 122.5 mM potassium gluconate, 12.5 mMKCl, 0.2 mM EGTA, 10 mM Hepes, 2 mM MgATP, 0.3 mM Na₃GTP and 8 mM NaCladjusted to pH 7.3 with KOH. Data was acquired with pClamp 10.2(Molecular Devices); current was filtered at 0.1 kHz and digitized at 2kHz. Cells with neuronal morphology with round cell body were selectedfor whole-cell patch clamp. Resting membrane potentials were monitoredimmediately after breaking-in in current-clamp mode. Thereafter, cellswere kept at a membrane potential of −60 mV to −80 mV, and 500 mscurrents were injected from −20 pA to +90 pA with 10 pA increments toinduce action potentials. For rebound depolarizations the cells wereinjected with a train of small currents of 20 pA to induce actionpotentials. Spontaneous post-synaptic currents were recorded at restingmembrane potentials using the same internal solution.

It was verified that the cells gave rise to neurons which evoked actionpotentials when assessed by patch clamp electrophysiology (11/11). Inthe mature fraction of neurons (resting membrane potential <−40 mV), 4out of 7 cells further showed rebound action potentials after briefdepolarization, which is characteristic of midbrain dopamine neurons invitro. FIG. 8H is representative of the trace of action potentialsinduced with depolarizing current injections. FIG. 8I is a graphillustrating that some ventral mesencephalon cells showed spontaneouspost-synaptic currents indicative of synaptic integration in the dish.FIG. 8J is an example of rebound depolarization after brief membranedepolarization characteristic of a dopaminergic phenotype. FIG. 8K is aninset from FIG. 8J showing a respective trace on an expanded scale.

Example 10

To validate that the new protocol of FIG. 3 gave rise to purepopulations of ventral mesencephalon progenitors, cultures were stainedfor FOXA2 and LMX1A/B, and high co-localisation of the two proteins wasfound. FIG. 9A is a set of photographs after immunostaining theprogenitors, illustrating that the cultures differentiated showed a veryhigh overlap of LMX1A/FOXA2. FIG. 9B is a set of graphs following flowcytometry analysis, indicating the cultures contained on average 95%OTX2⁺/FOXA2⁺ progenitors on day 16 of differentiation.

To monitor batch-to-batch variations predictive of in vivo outcome, aqRT-PCR panel was designed implementing the new key predictive markers(EN1, SPRY1, PAX8, CNPY1, and ETV5). Human embryonic stem cells weredifferentiated according to the GMP protocol of Example 10, and thenassessed on day 16 of differentiation for correct rostro-caudal ventralmesencephalon patterning as well as markers to monitor for the presenceof any contaminating forebrain (FOXG1), hindbrain (HOXA2), or lateral(PAX6) cell populations. The specificities of all primers used in thepanel were verified in samples of sub-dissected human fetal tissueenumerated in Table 5 below.

TABLE 5 Gene Full Gene Name Primer Sequence (fwd/rev) AADC DDC (DOPAdecarboxylase) GGGGACCACAACATGCTGCTCC (SEQ ID NO: 1)AATGCACTGCCTGCGTAGGCTG (SEQ ID NO: 2) ACTB Beta-actin CCTTGCACATGCCGGAG(SEQ ID NO: 3) GCACAGAGCCTCGCCTT (SEQ ID NO: 4) BARHL1 BarH-likehomeobox 1 GTACCAGAACCGCAGGACTAAA (SEQ ID NO: 5) AGAAATAAGGCGACGGGAACAT(SEQ ID NO: 6) BARHL2 BarH-like homeobox 2 GGAGATTACGAGTAGCCGTGAG (SEQID NO: 7) AAGCTACGCTCCAGTTGATTGA (SEQ ID NO: 8) CORIN Corin, serinpeptidase CATATCTCCATCGCCTCAGTTG (SEQ ID NO: 9) GGCAGGAGTCCATGACTGT (SEQID NO: 10) CNPY1 Canopy FGF signaling regulator 1 TTGGCCTCTCAAACACCATTCT(SEQ ID NO: 11) GAGCGAAACAAAACGCAATCAC (SEQ ID NO: 12) EN1 Engrailed 1CGTGGCTTACTCCCCATTTA (SEQ ID NO: 13) TCTCGCTGTCTCTCCCTCTC (SEQ ID NO:14) ETV5 Ets Variant 5 TCATCCTACATGAGAGGGGGTT (SEQ ID NO: 15)GACTTTGCCTTCCAGTCTCTCA (SEQ ID NO: 16) FOXA2 Forkhead box A2CCGTTCTCCATCAACAACCT (SEQ ID NO: 17) GGGGTAGTGCATCACCTGTT (SEQ ID NO:18) FOXG1 Forkhead box G1 (BG1) TGGCCCATGTCGCCCTTCCT (SEQ ID NO: 19)GCCGACGTGGTGCCGTTGTA (SEQ ID NO: 20) FOXP2 Forkhead box P2ATGAGCACTCTAAGCAGCCAAT (SEQ ID NO: 21) GTTGCAGATGCAGCAGTTCTAC (SEQ IDNO: 22) GAPDH Glyceraldehyde-3-phosphate TTGAGGTCAATGAAGGGGTCdehydrogenase (SEQ ID NO: 23) GAAGGTGAAGGTCGGAGTCA (SEQ ID NO: 24) GBX2Gastrulation brain homeobox 2 GTTCCCGCCGTCGCTGATGAT (SEQ ID NO: 25)GCCGGTGTAGACGAAATGGCCG (SEQ ID NO: 26) HOXA2 Homeobox A2CGTCGCTCGCTGAGTGCCTG (SEQ ID NO: 27) TGTCGAGTGTGAAAGCGTCGAGG (SEQ ID NO:28) LMX1A Primers spanning 3′ UTR of LMX1A CGCATCGTTTCTTCTCCTCT (SEQ IDNO: 29) CAGACAGACTTGGGGCTCAC (SEQ ID NO: 30) LMX1B LIM homeoboxtranscription factor b CTTAACCAGCCTCAGCGACT (SEQ ID NO: 31)TCAGGAGGCGAAGTAGGAAC (SEQ ID NO: 32) NKX2.1 NK2 homeobox 1AGGGCGGGGCACAGATTGGA (SEQ ID NO: 33) GCTGGCAGAGTGTGCCCAGA (SEQ ID NO:34) NURR1 NR4a2 CAGGCGTTTTCGAGGAAAT (SEQ ID NO: 35) GAGACGCGGAGAACTCCTAA(SEQ ID NO: 36) OCT4 POU5F1 TCTCCAGGTTGCCTCTCACT (SEQ ID NO: 37)GTGGAGGAAGCTGACAACAA (SEQ ID NO: 38) OTX2 Orthodenticle homeobox 2ACAAGTGGCCAATTCACTCC (SEQ ID NO: 39) GAGGTGGACAAGGGATCTGA (SEQ ID NO:40) PAX8 Paired box 8 ATAGCTGCCGACTAAGCATTGA (SEQ ID NO: 41)ATCCGTGCGAAGGTGCTTT (SEQ ID NO: 42) PITX3 Paired-like homeodomain 3GGAGGTGTACCCCGGCTACTCG (SEQ ID NO: 43) GAAGCCAGAGGCCCCACGTTGA (SEQ IDNO: 44) SHH Sonic hedgehog CCAATTACAACCCCGACATC (SEQ ID NO: 45)AGTTTCACTCCTGGCCACTG (SEQ ID NO: 46) SIM1 Single-minded homolog 1AAAGGGGGCCAAATCCCGGC (SEQ ID NO: 47) TCCGCCCCACTGGCTGTCAT (SEQ ID NO:48) SIX3 SIX homeobox 3 ACCGGCCTCACTCCCACACA (SEQ ID NO: 49)CGCTCGGTCCAATGGCCTGG (SEQ ID NO: 50) SOX1 SRY (sex determining regionY)-box 1 GGGAAAACGGGCAAAATAAT (SEQ ID NO: 51) TTTTGCGTTCACATCGGTTA (SEQID NO: 52) SPRY1 Sprouty 1 GCCCTGGATAAGGAACAGCTAC (SEQ ID NO: 53)GCCGAAATGCCTAATGCAAAGA (SEQ ID NO: 54) TH Tyrosine hydroxylaseCGGGCTTCTCGGACCAGGTGTA (SEQ ID NO: 55) CTCCTCGGCGGTGTACTCCACA (SEQ IDNO: 56) WNT1 Wingless-type MMTV integration site GAGCCACGAGTTTGGATGTTfamily, member 1 (SEQ ID NO: 57) TGCAGGGAGAAAGGAGAGAA (SEQ ID NO: 58)

To assess the reproducibility and accuracy of the new GMP protocolcompared to the research-grade protocol, 34 research grade and 43 GMPventral mesencephalic batches were analyzed using the designed qRT-PCRpanel.

FIG. 9C is an image of comparing hESCs differentiated according to thetwo protocols. The hESCs were assessed for RNA expression on day 16 ofdifferentiation. Differentiations toward ventral forebrain (vFB) andventral hindbrain (vHB) were included as controls. Values werecolor-coded and normalized to the sample with the highest geneexpression for each gene.

While all batches of cells had very robust expression of OTX1, OTX2,LMX1A, LMX1B, and FOXA2, there was considerable variation in theexpression of caudal ventral mesencephalon markers PAX8, EN1, SPRY1, andETV5 between batches generated with the research-grade protocol. Theresearch grade cell batches generally tended to fall into twocategories: (i) cell batches with high levels of EN1, PAX8, ETV5, SPRY1,and HOXA2; or (ii) cell batches with low levels of EN1, PAX8, ETV5,SPRY1, and HOXA2, while only very few batches contained high levels ofcaudal ventral mesencephalon markers (EN1, PAX8, ETV5, SPRY1) in theabsence of HOXA2 expression.

These expression patterns indicated that the presence of hindbrain cells(HOXA2⁺) was necessary for induction of a full caudal ventralmesencephalic identity in the cultures generated by the research gradeprotocol, since the absence of hindbrain cells yielded cultures with apredominantly rostral ventral mesencephalic identity. In contrast,implementation of the new GMP protocol yielded batches of cells whichwere more homogenous and which did not contain high levels of HOXA2contamination.

Addition of FGF8b to the GMP protocol (day 9-16) caused robustly inducedhigh-level expression of caudal ventral mesencephalon markers (EN1,PAX8, ETV5, and SPRY1), which had been shown to be predictive of DAyield concomitantly with a reduction in the expression of markersnegatively correlated with high DA yield (CORIN and FOXP2). Thiscaudalisation took place in the absence of HOXA2 contamination. Whenassessing grafts from two clinically relevant cell lines (H9 and RC17)differentiated according to the GMP protocol of Example 10, it was foundthat both lines generated neuron rich grafts with a high number ofTH-expressing cells. FIG. 9D (H9) and FIG. 9E (RC17) are representativeimages of grafts from batches containing high levels of caudal ventralmesencephalon markers. These cells densely innervated the host striatum(see those labeled with D″ and E″) and expressed mature mesDA markers.The protocol had decreased hindbrain contamination and increasedexpression of caudal ventral mesencephalon markers, which werepredictive of a good graft outcome.

Example 11

To determine if the GMP protocol yielded cells with functionaldopaminergic activity in vivo and if the anterior versus caudal VMphenotypes were truly predictive of in vivo efficacy, the cells wereassessed by transplantation to an animal model of Parkinson's Disease.Two groups of rats subjected to unilateral 6-OHDA lesions were assessedfor amphetamine-induced rotations before and after intrastriataltransplantation with VM-patterned RC17 cells differentiated according tothe LN-111 GMP protocol (protocol in FIG. 2). One group of animals(mesDA RC17) received cells differentiated in the presence of FGF8b fromday 9-16 to yield caudal VM mesDA progenitors expressing high levels ofpredictive markers EN1, CNPY1, SPRY1, ETV5 and PAX8 as shown in FIG. 9C.As exhibited in FIG. 10, this group of animals exhibited functionalrecovery as evidenced by reversal and overcompensation (by week 22) ofamphetamine-induced rotations. A decrease in rotations is equivalent tobehavioral recovery, as the lesions cause rotation in the rats. If thegraft is functional, the rotational behavior is abolished. In contrast,animals receiving cells differentiated in the absence of FGF8b to yieldrostral VM cells of the STN domain (STN RC17 group) did not exhibitfunctional recovery of amphetamine-induced rotations. TheseSTN-patterned cells expressed high levels of general VM markers but lowlevels of predictive caudal VM markers, thereby validating the power ofthe caudal VM markers for predicting in vivo outcome in animal models ofParkinson's Disease.

DISCUSSION

Pre-clinical evaluation of cells and their in vivo performance ispertinent because for disorders of the central nervous system,transplantation is performed with immature progenitor cells that undergoterminal differentiation and maturation after transplantation in vivo.Transplanted progenitors only become functional after several months invivo. This complicates the assessment of the therapeutic potential ofthe cells prior to grafting. It is thus desirable to be able to predictthe in vivo maturation of grafted cells based on in vitrocharacteristics of the progenitors prior to grafting.

It was found that in vitro differentiation into TH+ neurons does notcorrelate with the formation of TH+ neurons in vivo. It was also foundthat although FOXA2, LMX1A and CORIN, which are commonly used toidentify mesDA progenitors during development and in stem cell cultures,are necessary for dopamine differentiation after transplantation, theyare not sufficient to predict yield or functionality of the cells invivo. This highlights the need to validate markers that can predictfunctional maturation of the cell in vivo, rather than relying solely onmarkers expressed in the differentiating progenitors of a specific celllineage.

When applying an unbiased approach to identifying predictive markers ofsuccessful graft outcome, it was found that markers expressed bymidbrain cells close to the MHB (i.e. EN1, ETV5, CNPY1, PAX8 and SPRY1)correlated with a successful graft outcome, while markers expressed inthe diencephalic domain, such as EPHA3, showed a negative correlationwith graft outcome. These findings are in line with a recent study inthe mouse model showing a remarkably close relationship between mesDAand STN neuronal lineages. Whereas many key transcription factors,including LMX1A, LMX1B, CORIN, FOXA1, FOXA2, FOXP1, FOXP2, MSX1, NURR1,and PBX1, are shared by both lineages, only the mesDA lineage isidentified by expression of EN1 and CNPY1, which are restricted to thecaudal part of the ventral mesencephalon.

Based on analyzing these markers, it was confirmed that the ventralmesencephalic-patterned cultures contained both STN and mesDAprogenitors and that their relative proportion in each batch likelycontributed to the observed, but previously unexplained, variation in invivo outcome when progenitors defined only by high co-expression ofLMX1A, FOXA2 and OTX2 were transplanted.

Fine tuning the patterning to enrich for dopaminergic progenitors wasachieved via timed, exogenous delivery of FGF8b at the progenitor stageof differentiation. This, as well as a number of adjustments, allowedthe generation of a full GMP differentiation protocol for the productionof mesDA progenitors. Key to this GMP protocol is the use of LN-111, aphysiologically relevant extracellular matrix component that is normallyexpressed in the developing brain and which was found to supportattachment of differentiating neural progenitors but not pluripotentstem cells.

From post-mortem brain analysis of Parkinson's Disease patientstransplanted with human fetal ventral mesencephalic tissue, it wasdetermined that grafts containing approximately 100,000 transplanted TH+neurons are associated with significant clinical benefit in patients.Using the laminin-based GMP protocol, the number of mesDA progenitorsobtained per hESC at start of differentiation was greatly increasedcompared to the research grade protocol, and resulted in graft outcomesmatching the best differentiations from the research grade protocol.Given an average yield of about 5000 to 6000 mature DA neurons per100,000 transplanted progenitors from cell batches high in thepredictive markers, manual production of cells for several hundredpatients can be achievable even in small GMP labs without the need forautomated culture systems. The protocol presented here omits many of thelarge-scale production issues associated with other stem cell therapiesgoing into a clinic.

Further, the in vivo efficacy of the GMP protocol as well as thepredictive powers of the newly identified markers listed above wereverified in Example 11 and FIG. 10. A decrease in rotations wasconsidered equivalent to behavioral recovery, as the dopaminergic 6-OHDAlesions caused animals to rotate. A graft was considered functional ifit abolished the rotational behavior down to or below the baseline of 0.

The global gene profiling of a large number of cell batches that havebeen transplanted into a rat model allowed the establishment of a panelof markers to much more precisely predict a successful graft outcome atthe progenitor stage in vitro. The ability to better predict graftoutcome will accelerate the progression of stem cells towards clinicaluse and can be used for batch-to-batch comparability as well as tocompare the cells grafted in different clinical trials. In the longterm, a better prediction of in vivo maturation and functionalproperties of the cells already at the progenitor level will facilitatethe use of autologous or individually matched cells for transplantation.

It will be appreciated that variants of the above-disclosed and otherfeatures and functions, or alternatives thereof, may be combined intomany other different systems or applications. Various presentlyunforeseen or unanticipated alternatives, modifications, variations orimprovements therein may be subsequently made by those skilled in theart which are also intended to be encompassed by the following claims.

1. A method for providing caudalized dopaminergic progenitor cells witha high probability of successful graft outcome, comprising: platingembryonic stem cells on a first substrate coated with laminin-111,laminin-121, laminin-521, laminin-421, or laminin-511 to producedopaminergic progenitor cells; identifying dopaminergic progenitor cellsthat express caudal ventral midbrain markers; and isolating theidentified dopaminergic progenitor cells from the other dopaminergicprogenitor cells on the substrate to obtain the caudalized dopaminergicprogenitor cells with a high probability of successful graft outcome. 2.The method of claim 1, further comprising grafting the caudalizeddopaminergic progenitor cells into a brain of a mammal.
 3. The method ofclaim 2, wherein the mammal is a human; or where the grafting isperformed for the treatment of a neurodegenerative disease, such asParkinson's disease.
 4. The method of claim 1, wherein the step ofidentifying dopaminergic progenitor cells is performed by identifyingcells that express high levels of EN1, SPRY1, WNT1, CNPY1, PAX8, ETV5,PAX5, FGF8, SPS, or TLE4 or wherein the step of identifying dopaminergicprogenitor cells is performed by identifying cells that express highlevels of EN1, SPRY1, PAX8, CNPY1, and ETV5; or wherein the step ofidentifying dopaminergic progenitor cells further includes excludingcells that express high levels of EPHA3, FEZF1, or WNT7B.
 5. The methodof claim 1, further comprising identifying and excluding dopaminergicprogenitor cells that express high levels of BARHL1, BARHL2, FOXG1,SIX3, HOXA2, GBX2, or PAX6.
 6. A method for inducing production ofcaudalised ventral mesencephalon progenitor cells, comprising: platingembryonic stem cells onto a substrate containing laminin-111,laminin-421, laminin-511, or laminin-521 to produce the caudalisedventral mesencephalon progenitor cells.
 7. The method of claim 6,wherein the stem cells are cultured in a primary medium comprising N2medium, a TGF-β inhibitor, noggin, sonic hedgehog protein, and a GSK3inhibitor, and which does not contain B27 supplement.
 8. The method ofclaim 7, wherein the primary medium is removed and a secondary medium isadded, the secondary medium comprising N2 medium and a fibroblast growthfactor (FGF), and which does not contain B27 supplement.
 9. The methodof claim 8, wherein the FGF is FGF8b; or wherein the secondary medium isadded about 156 hours to about 228 hours after the plating.
 10. Themethod of claim 8, wherein the secondary medium is removed and the stemcells are replated.
 11. The method of claim 10, wherein the replatingoccurs about 252 hours to about 276 hours after the plating; or whereinthe replating occurs using a tertiary medium that comprises a B27medium, a ROCK inhibitor, the FGF, a brain derived neurotrophic factor(BDNF), and ascorbic acid.
 12. The method of claim 10, wherein the stemcells are then cultured in a quaternary medium, the quaternary mediumcomprising a B27 medium, the FGF, a brain derived neurotrophic factor(BDNF), and ascorbic acid.
 13. The method of claim 12, wherein the stemcells are cultured in the quaternary medium until about 324 hours toabout 396 hours after the plating; or wherein the stem cells arecultured in the quaternary medium for a time period of about 108 hoursto about 132 hours.
 14. A method for inducing production of dopaminergiccells, comprising: plating pluripotent stem cells on a substrate coatedwith laminin-111, laminin-121, laminin-521, laminin-421, or laminin-511to produce the dopaminergic cells.
 15. The method of claim 14, whereinthe cells are passaged with EDTA prior to the plating.
 16. The method ofclaim 14, wherein the cells are cultured in a first medium comprising aneural induction medium or an N2 medium; a ROCK inhibitor; a TGF-βinhibitor; and a GSK3 inhibitor.
 17. The method of claim 16, wherein thefirst medium is removed and a second medium is added, the second mediumcomprising a neural induction medium or an N2 medium; a TGF-β inhibitor,and a GSK3 inhibitor, and not containing a ROCK inhibitor.
 18. Themethod of claim 17, wherein the second medium is added about 36 hours toabout 60 hours after the plating.
 19. The method of claim 17, whereinthe second medium further contains about 0.2 μM or more of the GSK3inhibitor and about 50 ng/mL or more of the sonic hedgehog protein; orwherein the second medium contains about 0.2 μM to about 0.4 μM of theGSK3 inhibitor for diencephalic fates; or wherein the second mediumcontains about 0.6 μM to about 0.8 μM of the GSK3 inhibitor formesencephalic fates; or wherein the second medium contains about 1 μM toabout 2 μM of the GSK3 inhibitor for anterior rhomencephalic fates; orwherein the second medium contains at least 4 μM of the GSK3 inhibitorfor posterior rhomencephalic fates; or wherein the first medium and thesecond medium comprise about 50 ng/mL to about 150 ng/mL of the sonichedgehog protein for basal plate fates; or wherein the first medium andthe second medium contains at least 200 ng/m L of the sonic hedgehogprotein for floor plate fates; or wherein bone morphogenic proteininhibitors are not present in the second medium after day 4 for roofplate fates.
 20. The method of claim 17, wherein the second medium isremoved and a third medium is added, the third medium comprising (i) aneural proliferation medium or an N2 medium; and (ii) a TGF-β inhibitor,and optionally also contains sonic hedgehog protein.
 21. The method ofclaim 20, wherein the third medium is added about 84 hours to about 108hours after the plating; or wherein the third medium is also renewedabout 156 hours to about 180 hours after the plating.
 22. The method ofclaim 20, wherein the third medium is replaced with a fourth mediumcomprising (i) a neural proliferation medium (NPM) or an N2 medium; and(ii) a fibroblast growth factor (FGF).
 23. The method of claim 22,wherein the fourth medium is added about 156 hours to about 228 hoursafter the plating; or wherein the FGF is FGF8b.
 24. The method of claim22, wherein the cells are replated on a second plate coated withlaminin-111, laminin-121, laminin-521, laminin-421, or laminin-511. 25.The method of claim 24, wherein the cells are replated about 252 hoursto about 276 hours after the original plating.
 26. The method of claim24, wherein the replated cells are cultured in a fifth medium comprisinga B27 medium; a brain derived neurotrophic factor (BDNF); ascorbic acid(AA); a glial cell line-derived neurotrophic factor (GDNF); and afibroblast growth factor (FGF).
 27. The method of claim 26, wherein thefifth medium is renewed about 324 hours to about 348 hours after theplating.
 28. The method of claim 14, wherein after production, thedopaminergic cells are maintained on laminin-111, laminin-121,laminin-521, laminin-421, or laminin-511 until transplantation orcryopreservation.
 29. A cell culture kit for inducing production ofdopaminergic cells in vitro, comprising: a cell culture plate with acoating of laminin-111, laminin-121, laminin-521, laminin-421, orlaminin-511; and a cell culture medium; a GSK3 inhibitor; sonic hedgehogprotein; a ROCK inhibitor; a TGF-β inhibitor; a fibroblast growth factor(FGF); a brain derived neurotrophic factor (BDNF); and ascorbic acid(AA).